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Create design matrix for differential methylation analysis
Annotation annotate DifferentialMethylation minfiDataEPIC
updated 21 months ago by ▴ 780 • written 21 months ago by • 0
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2
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 2.2 years ago by ▴ 70 • written 2.2 years ago by ▴ 140
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8
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fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 19 months ago by • 0 • written 2.3 years ago by • 0
4
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3
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SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.9 years ago by 68k • written 2.9 years ago by ▴ 10
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
3.0 years ago Palmira • 0
1
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2
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3.9k
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mapping mouse ENSEMBL ids to human gene symbol
Annotation AnnotationDbi annotate
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
2
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1
reply
895
views
The best pacakge to annotate a set of regions
annotate
updated 4.7 years ago by 68k • written 4.7 years ago by ▴ 20
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4
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1.9k
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Annotating a sequence, new to bioconductor
annotate
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
0
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3
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1.5k
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How to annotate gene ontologies based on Gene Symbols in R
GO.db annotate
7.4 years ago • updated 7.3 years ago dusan.petrovic • 0
0
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1
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1.6k
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RNAseq _generating tx2gene table and using kallisto output to run DEseq
deseq annotate
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
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4
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8.5k
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How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
oligo annotate
7.6 years ago llkxiaolan ▴ 10
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1
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3.3k
views
How many genes are appropriate for GO enrichment analysis
go annotate rna-seq clusterprofiler
updated 7.7 years ago by ▴ 120 • written 7.7 years ago by ▴ 20
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1
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1.8k
views
querying annotation hub for common TF, in common cell line returns no results....
annotate annotationhub
updated 7.8 years ago by 4.2k • written 7.8 years ago by ▴ 50
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8
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Can't find Ly76 on my Affymetrix MoGene 2.0ST array annotated with pd.mogene.2.0.st package
pd.mogene.2.0.st mogene20sttranscriptcluster.db annotate
updated 7.9 years ago by 68k • written 7.9 years ago by • 0
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3
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2.7k
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Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 8.0 years ago by ▴ 370 • written 8.1 years ago by ▴ 10
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1
reply
1.6k
views
Annotation of Probe id to Gene
bioconductor annotate microarray arabidopsis thaliana
updated 8.0 years ago by 68k • written 8.0 years ago by • 0
0
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4
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1.7k
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TimmR error for hgu133a.db
software error annotate hgu133a
updated 8.3 years ago by 68k • written 8.3 years ago by • 0
3
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6
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3.2k
views
RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation microarray annotate annotationforge
8.4 years ago MOD • 0
6
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5
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15k
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Installation of package DESeq2
deseq2 rcurl annotate genefilter geneplotter
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 10
1
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2
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2.6k
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blastSequences queries failing due to BLAST switch to https?
annotate blastSequences BLAST https
updated 8.8 years ago by 25k • written 8.8 years ago by • 0
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2
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1.9k
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Problems using intansv...
annotate annotate
updated 9.1 years ago by • 0 • written 11.2 years ago by ▴ 10
2
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1
reply
1.3k
views
Use matchPattern for large DNAStrings
biostrings annotate
updated 9.1 years ago by 16k • written 9.1 years ago by ▴ 40
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1
reply
1.8k
views
How to identify the microarray annotation library automatically from GEO study ID?
limma microarray annotation bioconductor annotate
updated 9.2 years ago by 68k • written 9.2 years ago by • 0
0
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1
reply
1.8k
views
Getting data on the out-of-frame transcripts
annotate sequencing genomicfeatures
updated 9.9 years ago by 16k • written 10.0 years ago by • 0
0
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1
reply
2.4k
views
Difference in TxDb.Hsapiens.UCSC.hg19.knownGene and UCSC knownGene
annotate exons txdb.hsapiens.ucsc.hg19.knowngene
10.0 years ago adnan.niazi • 0
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1
reply
1.5k
views
.getNcbiURL returns old NCBI url ?
annotate ncbi url
10.5 years ago reuma • 0
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1
reply
2.0k
views
can't run functions in 'annotate'
annotate
10.6 years ago boris.steipe • 0
1
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2
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1.9k
views
about library(Homo.sapiens) from TxDb.Hsapiens.UCSC.hg18.knownGene
annotate
10.6 years ago Bogdan ▴ 670
2
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2
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2.2k
views
BLAST export library 'annotate'
blast annotate biostrings export fasta
10.7 years ago b.stielow • 0
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2
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12k
views
Probe to gene id conversion
annotate biomart probe to gene id
updated 10.7 years ago by 68k • written 10.7 years ago by ▴ 20
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6
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2.7k
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Missing as.list generic from AnnotationDbi?
annotate AnnotationDbi annotate AnnotationDbi
updated 10.8 years ago by ★ 2.0k • written 12.1 years ago by ★ 7.9k
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2
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2.2k
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Bioconductor Digest, Vol 138, Issue 27
annotate biovizBase ggbio UniProt.ws Pbase annotate biovizBase ggbio UniProt.ws Pbase
updated 10.9 years ago by ▴ 490 • written 10.9 years ago by 1.6k
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1
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1.7k
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Positional Details with Features through UniProt.ws Ultimately to display as tracks in ggbio
annotate ggbio annotate ggbio
updated 10.9 years ago by ▴ 490 • written 10.9 years ago by ▴ 30
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ChIPpeakAnno
SNP Annotation annotate convert SNP Annotation annotate convert
10.9 years ago Julie Zhu ★ 4.3k
0
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1
reply
1.6k
views
non-CpG methylated regions and strand information in MEDIPS output
BSgenome annotate biomaRt BSgenome MEDIPS BSgenome annotate biomaRt BSgenome MEDIPS
updated 10.9 years ago by ▴ 570 • written 10.9 years ago by ★ 13k
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1
reply
2.2k
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annotation for TAqman assay IDs
Annotation probe annotate Annotation probe annotate
updated 11.0 years ago by 68k • written 11.0 years ago by ▴ 10
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2
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1.8k
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Affymetrix mouse 430_2 array - annotation problem
Annotation mouse4302 annotate Annotation mouse4302 annotate
updated 11.0 years ago by 68k • written 11.0 years ago by ▴ 550
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5
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4.8k
views
annotating microarray data with mogene10stv1
Microarray Annotation annotate limma ASSIGN Microarray Annotation annotate limma ASSIGN
updated 11.0 years ago by 68k • written 11.0 years ago by ▴ 70
0
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2
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3.3k
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Biomart annotation
annotate convert annotate convert
updated 11.0 years ago by ▴ 190 • written 11.0 years ago by ▴ 40
0
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5
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3.0k
views
Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets
Annotation probe annotate annaffy oligo ReportingTools Annotation probe annotate annaffy
updated 11.1 years ago by ▴ 160 • written 11.1 years ago by 68k
1
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8
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4.4k
views
GRanges apply functions
GO annotate GO annotate
updated 11.1 years ago by ★ 4.2k • written 11.1 years ago by ▴ 380
0
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1
reply
4.1k
views
ChIPseeker: Error in annotatePeak
Sequencing GO annotate ChIPseeker Sequencing GO annotate ChIPseeker
11.2 years ago António Miguel de Jesus Domingues ▴ 510
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1
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1.9k
views
ChIPpeakAnno
annotate ChIPpeakAnno annotate ChIPpeakAnno
updated 11.2 years ago by ★ 4.3k • written 11.2 years ago by ▴ 350
0
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1.2k
views
lumi-package problem: nuID [e.g. nuID2EntrezID()] from vignette example throws an error on my system
annotate annotate
11.3 years ago Guest User ★ 13k
2
votes
1
reply
1.6k
views
HTqPCR- gene names not maintained in limmaCtData
annotate ddCt HTqPCR annotate ddCt HTqPCR
11.4 years ago Cornwell, Adam ▴ 110
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9
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2.4k
views
variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
VariantAnnotation Cancer Yeast annotate Biostrings VariantAnnotation VariantAnnotation
updated 11.4 years ago by 16k • written 11.4 years ago by ▴ 740
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0
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1.2k
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Ontology
Annotation GO annotate GOstats Annotation GO annotate GOstats
11.4 years ago Marc Carlson ★ 7.2k
0
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0
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1.5k
views
zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
VariantAnnotation Annotation PolyPhen SIFT annotate VariantAnnotation ensemblVEP Annotation
11.6 years ago Valerie Obenchain ★ 6.8k
0
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5
replies
1.9k
views
multiple annotations with get()?
Biobase annotate convert Biobase annotate convert
updated 11.8 years ago by 21k • written 11.8 years ago by ▴ 230
0
votes
2
replies
1.8k
views
limma_3.17.23 - missing ILMN identifiers in EList objects after read.ilmn
Annotation Normalization GO probe annotate Annotation Normalization GO probe annotate
updated 11.8 years ago by ★ 3.6k • written 11.8 years ago by ▴ 120
50 results • Page 1 of 1
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Answer: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by Aaron Lun ★ 28k
Consider using a `SVT_SparseMatrix` from the **SparseArray** package, which is explicitly designed for this. **DropletUtils** (in BioC-deve…
Comment: Regarding the issue of background genes in enrichment analysis by zalinkaelisa • 0
Use good features to distinguish the situation of the type of experiment [baseball 9][1] [1]: https://baseball9.io/
Comment: Heatmap of the Count Matrix by gta5movilecom • 0
Using it for the top 20 genes in the heatmap highlights high-expression genes, but may miss out on variance-driven patterns. If you want to…
Answer: Regarding the issue of background genes in enrichment analysis by ATpoint ★ 4.9k
It should imo be the genes that were eligable to yield a "significant" result in your analysis. So, if you test set is derived from differe…
Comment: Applying lmFit(), eBayes() and topTable() for modeling associations between NMR- by Gordon Smyth 52k
> How do these logFC values compare to standard effect sizes derived using a basic regression model like lm()? Exactly the same. Both soft…
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Regarding the issue of background genes in enrichment analysis
Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
Comment: How can I avoid artifacts in gene set/pathway scoring by UCell and similar algor
Answer: I would like to perform differential expression analysis of lncRNAs using DESeq2
I would like to perform differential expression analysis of lncRNAs using DESeq2 and edgeR.
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