Bioconductor Code: basecallQC

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A Wokaty authored on 15/04/2025 15:10:19
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.32.0
                                     +Version: 1.33.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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A Wokaty authored on 15/04/2025 15:10:19
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.31.0
                                     +Version: 1.32.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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J Wokaty authored on 29/10/2024 14:18:46
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.30.0
                                     +Version: 1.31.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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J Wokaty authored on 29/10/2024 14:18:46
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.29.0
                                     +Version: 1.30.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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J Wokaty authored on 30/04/2024 14:57:34
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.28.0
                                     +Version: 1.29.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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J Wokaty authored on 30/04/2024 14:57:34
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.27.0
                                     +Version: 1.28.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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J Wokaty authored on 24/10/2023 14:56:44
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.26.0
                                     +Version: 1.27.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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J Wokaty authored on 24/10/2023 14:56:44
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.25.0
                                     +Version: 1.26.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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J Wokaty authored on 25/04/2023 14:53:38
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.24.0
                                     +Version: 1.25.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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J Wokaty authored on 25/04/2023 14:53:38
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.23.0
                                     +Version: 1.24.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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J Wokaty authored on 01/11/2022 15:15:31
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.22.0
                                     +Version: 1.23.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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J Wokaty authored on 01/11/2022 15:15:31
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.21.0
                                     +Version: 1.22.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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Nitesh Turaga authored on 26/04/2022 15:40:14
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.20.0
                                     +Version: 1.21.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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Nitesh Turaga authored on 26/04/2022 15:40:14
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.19.0
                                     +Version: 1.20.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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Nitesh Turaga authored on 26/10/2021 16:34:33
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.18.0
                                     +Version: 1.19.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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Nitesh Turaga authored on 26/10/2021 16:34:33
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.17.0
                                     +Version: 1.18.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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Nitesh Turaga authored on 19/05/2021 16:27:10
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.16.0
                                     +Version: 1.17.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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Nitesh Turaga authored on 19/05/2021 16:27:10
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.15.0
                                     +Version: 1.16.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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Nitesh Turaga authored on 27/10/2020 15:23:18
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.14.0
                                     +Version: 1.15.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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Nitesh Turaga authored on 27/10/2020 15:23:18
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.13.0
                                     +Version: 1.14.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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Nitesh Turaga authored on 27/04/2020 19:06:59
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.12.0
                                     +Version: 1.13.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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Nitesh Turaga authored on 27/04/2020 19:06:59
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.11.1
                                     +Version: 1.12.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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ThomasCarroll authored on 04/04/2020 17:13:15
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.11.0
                                     +Version: 1.11.1
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.
@@ -24,4 +24,4 @@ Collate:
                                        tables.R
                                        FastQCShortRead_Functions.R
                                        processInterOps_Functions.R
                                     -RoxygenNote: 6.0.1
                                     +RoxygenNote: 7.1.0

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Nitesh Turaga authored on 29/10/2019 17:42:18
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.10.0
                                     +Version: 1.11.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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Nitesh Turaga authored on 29/10/2019 17:10:22
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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.9.0
                                     +Version: 1.10.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

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Nitesh Turaga authored on 02/05/2019 16:14:46
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DESCRIPTION

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@@ -1,7 +1,7 @@
                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.8.0
                                     +Version: 1.9.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:54:06
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DESCRIPTION

History View file @ 0f68565

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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.7.0
                                     +Version: 1.8.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:37
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DESCRIPTION

History View file @ 33f4312

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                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.6.0
                                     +Version: 1.7.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:42:04
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DESCRIPTION

History View file @ 2a64547

@@ -1,7 +1,7 @@
                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.5.0
                                     +Version: 1.6.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:41:43
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DESCRIPTION

History View file @ f8f3127

@@ -1,7 +1,7 @@
                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.4.0
                                     +Version: 1.5.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:35:46
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DESCRIPTION

History View file @ 91bb781

@@ -1,7 +1,7 @@
                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.3.1
                                     +Version: 1.4.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

Browse code

.

Thomas Carroll authored on 23/04/2018 20:13:46
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DESCRIPTION

History View file @ 8aac03d

@@ -1,27 +1,27 @@
                                     -Package: basecallQC
                                     -Type: Package
                                     -Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.3.0
                                     -Author: Thomas Carroll and Marian Dore
                                     -Maintainer: Thomas Carroll <[email protected]>
                                     -Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.
                                     -LazyData: TRUE
                                     -biocViews: Sequencing, Infrastructure, DataImport, QualityControl
                                     -License: GPL (>= 3)
                                     -Depends: R (>= 3.4), stats, utils, methods, rmarkdown, knitr, prettydoc, yaml
                                     -Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead
                                     -Suggests: testthat, BiocStyle
                                     -VignetteBuilder: knitr
                                     -SystemRequirements: bcl2Fastq (versions >= 2.1.7)
                                     -Collate:
                                     -  processIlluminaSamplesheets_Functions.R
                                     -  processXMLs_Functions.R
                                     -  allClasses.R
                                     -  allMethods.R
                                     -  processExternalFormats_Functions.R
                                     -  plots.R
                                     -  reporting.R
                                     -  tables.R
                                     -  FastQCShortRead_Functions.R
                                     -  processInterOps_Functions.R
                                     -RoxygenNote: 6.0.1
                                     +Package: basecallQC
                                     +Type: Package
                                     +Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     +Version: 1.3.1
                                     +Author: Thomas Carroll and Marian Dore
                                     +Maintainer: Thomas Carroll <[email protected]>
                                     +Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.
                                     +LazyData: TRUE
                                     +biocViews: Sequencing, Infrastructure, DataImport, QualityControl
                                     +License: GPL (>= 3)
                                     +Depends: R (>= 3.4), stats, utils, methods, rmarkdown, knitr, prettydoc, yaml
                                     +Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead
                                     +Suggests: testthat, BiocStyle
                                     +VignetteBuilder: knitr
                                     +SystemRequirements: bcl2Fastq (versions >= 2.1.7)
                                     +Collate:
                                     +  processIlluminaSamplesheets_Functions.R
                                     +  processXMLs_Functions.R
                                     +  allClasses.R
                                     +  allMethods.R
                                     +  processExternalFormats_Functions.R
                                     +  plots.R
                                     +  reporting.R
                                     +  tables.R
                                     +  FastQCShortRead_Functions.R
                                     +  processInterOps_Functions.R
                                     +RoxygenNote: 6.0.1

Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:54:31
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DESCRIPTION

History View file @ b81ff49

@@ -1,7 +1,7 @@
                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.2.0
                                     +Version: 1.3.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:41:27
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DESCRIPTION

History View file @ 967a5d5

@@ -1,7 +1,7 @@
                                      Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     -Version: 1.1.1
                                     +Version: 1.2.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

Browse code

Fixes and updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/basecallQC@130196 bc3139a8-67e5-0310-9ffc-ced21a209358

Tom Carroll authored on 08/06/2017 16:16:28
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DESCRIPTION

History View file @ 5e9aab2

@@ -1,33 +1,27 @@
                                     -Package: basecallQC
                                     -Type: Package
                                     -Title: Working with Illumina Basecalling and Demultiplexing input and
                                     -        output files
                                     -Version: 1.1.0
                                     -Author: Thomas Carroll and Marian Dore
                                     -Maintainer: Thomas Carroll <[email protected]>
                                     -Description: The basecallQC package provides tools to work with
                                     -        Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to
                                     -        basecalling and demultiplexing using the bcl2Fastq software,
                                     -        basecallQC functions allow the user to update Illumina sample
                                     -        sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean
                                     -        sample sheets of common problems such as invalid sample names
                                     -        and IDs, create read and index basemasks and the bcl2Fastq
                                     -        command. Following the generation of basecalled and
                                     -        demultiplexed data, the basecallQC packages allows the user to
                                     -        generate HTML tables, plots and a self contained report of
                                     -        summary metrics from Illumina XML output files.
                                     -LazyData: TRUE
                                     -biocViews: Sequencing, Infrastructure, DataImport, QualityControl
                                     -License: GPL (>= 3)
                                     -Depends: R (>= 3.4), stats, utils, methods, rmarkdown, knitr,
                                     -        prettydoc, yaml
                                     -Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr,
                                     -        magrittr, DT, lazyeval, ShortRead
                                     -Suggests: testthat, BiocStyle
                                     -VignetteBuilder: knitr
                                     -SystemRequirements: bcl2Fastq (versions >= 2.1.7)
                                     -Collate: processIlluminaSamplesheets_Functions.R
                                     -        processXMLs_Functions.R allClasses.R allMethods.R
                                     -        processExternalFormats_Functions.R plots.R reporting.R tables.R
                                     -        FastQCShortRead_Functions.R
                                     -RoxygenNote: 6.0.1
                                     +Package: basecallQC
                                     +Type: Package
                                     +Title: Working with Illumina Basecalling and Demultiplexing input and output files
                                     +Version: 1.1.1
                                     +Author: Thomas Carroll and Marian Dore
                                     +Maintainer: Thomas Carroll <[email protected]>
                                     +Description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.
                                     +LazyData: TRUE
                                     +biocViews: Sequencing, Infrastructure, DataImport, QualityControl
                                     +License: GPL (>= 3)
                                     +Depends: R (>= 3.4), stats, utils, methods, rmarkdown, knitr, prettydoc, yaml
                                     +Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead
                                     +Suggests: testthat, BiocStyle
                                     +VignetteBuilder: knitr
                                     +SystemRequirements: bcl2Fastq (versions >= 2.1.7)
                                     +Collate:
                                     +  processIlluminaSamplesheets_Functions.R
                                     +  processXMLs_Functions.R
                                     +  allClasses.R
                                     +  allMethods.R
                                     +  processExternalFormats_Functions.R
                                     +  plots.R
                                     +  reporting.R
                                     +  tables.R
                                     +  FastQCShortRead_Functions.R
                                     +  processInterOps_Functions.R
                                     +RoxygenNote: 6.0.1

Browse code

bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/basecallQC@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:50:57
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DESCRIPTION

History View file @ 12c0db4

@@ -2,7 +2,7 @@ Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and
                                              output files
                                     -Version: 1.0.0
                                     +Version: 1.1.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with

Browse code

bump x.y.z versions to even y prior to creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/basecallQC@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:25:24
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DESCRIPTION

History View file @ ba1d073

@@ -2,7 +2,7 @@ Package: basecallQC
                                      Type: Package
                                      Title: Working with Illumina Basecalling and Demultiplexing input and
                                              output files
                                     -Version: 0.99.1
                                     +Version: 1.0.0
                                      Author: Thomas Carroll and Marian Dore
                                      Maintainer: Thomas Carroll <[email protected]>
                                      Description: The basecallQC package provides tools to work with

Browse code

Adding RaggedExperiment, basecallQC, CATALYST, GenomicScores, IMAS, semisup, ImpulseDE2, methylInheritance, biotmle, biotmleData, BLMA, TCGAWorkflow, metavizr

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/basecallQC@128350 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 07/04/2017 20:14:00
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DESCRIPTION

History View file @ 82d9bc8

                                     new file mode 100644
@@ -0,0 +1,33 @@
                                     +Package: basecallQC
                                     +Type: Package
                                     +Title: Working with Illumina Basecalling and Demultiplexing input and
                                     +        output files
                                     +Version: 0.99.1
                                     +Author: Thomas Carroll and Marian Dore
                                     +Maintainer: Thomas Carroll <[email protected]>
                                     +Description: The basecallQC package provides tools to work with
                                     +        Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to
                                     +        basecalling and demultiplexing using the bcl2Fastq software,
                                     +        basecallQC functions allow the user to update Illumina sample
                                     +        sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean
                                     +        sample sheets of common problems such as invalid sample names
                                     +        and IDs, create read and index basemasks and the bcl2Fastq
                                     +        command. Following the generation of basecalled and
                                     +        demultiplexed data, the basecallQC packages allows the user to
                                     +        generate HTML tables, plots and a self contained report of
                                     +        summary metrics from Illumina XML output files.
                                     +LazyData: TRUE
                                     +biocViews: Sequencing, Infrastructure, DataImport, QualityControl
                                     +License: GPL (>= 3)
                                     +Depends: R (>= 3.4), stats, utils, methods, rmarkdown, knitr,
                                     +        prettydoc, yaml
                                     +Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr,
                                     +        magrittr, DT, lazyeval, ShortRead
                                     +Suggests: testthat, BiocStyle
                                     +VignetteBuilder: knitr
                                     +SystemRequirements: bcl2Fastq (versions >= 2.1.7)
                                     +Collate: processIlluminaSamplesheets_Functions.R
                                     +        processXMLs_Functions.R allClasses.R allMethods.R
                                     +        processExternalFormats_Functions.R plots.R reporting.R tables.R
                                     +        FastQCShortRead_Functions.R
                                     +RoxygenNote: 6.0.1