Bioconductor Code: atena

Graph of atena

9b1f68f (origin/RELEASE_3_21, RELEASE_3_21) Bump version by Robert Castelo <[email protected]> 2025-05-30 14:11:46 +0200;
21bf6f4 Bugfix on annotaTEs() to handle the case then LC_TIME is other than C or English, raised in issue #8. A few fixes on documentation links by Robert Castelo <[email protected]> 2025-05-30 14:06:21 +0200;
36fb9d2 (HEAD -> devel, origin/devel, origin/HEAD) Bump version by Robert Castelo <[email protected]> 2025-05-30 14:10:44 +0200;
2006d43 Bugfix on annotaTEs() to handle the case then LC_TIME is other than C or English, raised in issue #8. A few fixes on documentation links by Robert Castelo <[email protected]> 2025-05-30 14:06:21 +0200;
e11e684 bump x.y.z version to odd y following creation of RELEASE_3_21 branch by A Wokaty <[email protected]> 2025-04-15 12:38:43 -0400;
678448e bump x.y.z version to even y prior to creation of RELEASE_3_21 branch by A Wokaty <[email protected]> 2025-04-15 12:38:43 -0400;
7d6f186 Updated NEWS file and bumped version by Robert Castelo <[email protected]> 2025-04-14 19:29:11 +0200;
97fbc13 Use match.fun() in annotaTEs() to avoid triggering a cryptic error when parsefun is a character string by Robert Castelo <[email protected]> 2025-04-11 23:19:37 +0200;
8ebad87 (origin/RELEASE_3_20, RELEASE_3_20) Fixed GHA workflow by Robert Castelo <[email protected]> 2025-02-03 14:40:22 +0100;
a5b071f Updated GHA workflow by Robert Castelo <[email protected]> 2025-01-31 17:41:09 +0100;
90f5b5e Fixed GHA workflow by Robert Castelo <[email protected]> 2025-02-03 14:40:22 +0100;
2b13d77 Updated GHA workflow by Robert Castelo <[email protected]> 2025-01-31 17:41:09 +0100;
0778c4e (origin/master) bump x.y.z version to odd y following creation of RELEASE_3_20 branch by J Wokaty <[email protected]> 2024-10-29 11:04:19 -0400;
1f05752 bump x.y.z version to even y prior to creation of RELEASE_3_20 branch by J Wokaty <[email protected]> 2024-10-29 11:04:19 -0400;
404c873 bump x.y.z version to odd y following creation of RELEASE_3_19 branch by J Wokaty <[email protected]> 2024-04-30 11:37:21 -0400;
7e1c59e (origin/RELEASE_3_19, RELEASE_3_19) bump x.y.z version to even y prior to creation of RELEASE_3_19 branch by J Wokaty <[email protected]> 2024-04-30 11:37:21 -0400;
59e1a71 Updated NEWS file and package maintainer :' by Robert Castelo <[email protected]> 2024-04-27 16:37:20 +0200;
e814a13 Reduced execution time in some of the examples by Robert Castelo <[email protected]> 2024-04-24 13:54:58 +0200;
ad226bc Updated vignette, added progress reporting messages by Robert Castelo <[email protected]> 2024-04-24 09:12:58 +0200;
a09ae7d Updated documentation by Robert Castelo <[email protected]> 2024-04-22 12:30:09 +0200;
b720afb Several fixes, improvements in documentation by Robert Castelo <[email protected]> 2024-04-22 02:42:32 +0200;
e8a553a Combine examples of annotation TE class getters into a single one by Robert Castelo <[email protected]> 2024-04-21 15:01:33 +0200;
f6c1e2a Updated README.md by Robert Castelo <[email protected]> 2024-04-20 23:35:05 +0200;
f22c1d2 Updated GitHub URL in DESCRIPTION by Robert Castelo <[email protected]> 2024-04-20 23:10:53 +0200;
dd3a321 Various fixes and documentation improvements by Robert Castelo <[email protected]> 2024-04-20 17:19:42 +0200;
a5d1231 Added GenomicFeatures to imports in DESCRIPTION by Robert Castelo <[email protected]> 2024-04-19 16:16:13 +0200;
e6bcc39 Various fixes by Robert Castelo <[email protected]> 2024-04-18 21:21:12 +0200;
db720af bump x.y.z version to odd y following creation of RELEASE_3_18 branch by J Wokaty <[email protected]> 2023-10-24 11:36:26 -0400;
634a469 (origin/RELEASE_3_18, RELEASE_3_18) bump x.y.z version to even y prior to creation of RELEASE_3_18 branch by J Wokaty <[email protected]> 2023-10-24 11:36:26 -0400;
f67c375 bump x.y.z version to odd y following creation of RELEASE_3_17 branch by J Wokaty <[email protected]> 2023-04-25 11:32:49 -0400;
4053ecb (origin/RELEASE_3_17, RELEASE_3_17) bump x.y.z version to even y prior to creation of RELEASE_3_17 branch by J Wokaty <[email protected]> 2023-04-25 11:32:49 -0400;
4f89ec2 Updated NEWS file by beacalvo <[email protected]> 2023-04-20 17:57:00 +0200;
6258449 Changed default value of geneFeatures to NULL by beacalvo <[email protected]> 2023-04-05 23:15:12 +0200;
5bb0f35 Modified examples so that RepeatMasker annotations from AnnotationHub are used by beacalvo <[email protected]> 2023-04-04 15:01:22 +0200;
a7eed4b Simplified names of GRanges inside GRangesList of parsed TE annotations by beacalvo <[email protected]> 2023-04-04 12:45:24 +0200;
d554531 Updating annotaTEs() to address cases where there are more than one RepeatMasker annotation for a specific genome version by beacalvo <[email protected]> 2023-04-04 12:10:23 +0200;
176f3be Implemented alternative for rescale() in Telescope method to reduce dependencies by beacalvo <[email protected]> 2023-04-04 10:42:58 +0200;
f54938d Updated vignette to use parsed TE annotations to quantify TE expression, as well as Txdb for gene annotations. Fixed .processFeatures behaviour for when TE annotations are a GRangesList by beacalvo <[email protected]> 2023-04-04 10:40:33 +0200;
d6d806d Update check-bioc.yml to check the devel branch by Beatriz Calvo Serra <[email protected]> 2023-03-29 09:51:04 +0200;
f24df02 Fixed error in TEtranscripts unit test due to numerical instability by beacalvo <[email protected]> 2023-03-28 22:27:00 +0200;
36c06cc Added .matchSeqinfo(). Updated example annotation files. Updated RUnit tests by beacalvo <[email protected]> 2023-03-21 18:40:17 +0100;
4a1486f Addressed NOTEs from BiocCheck by beacalvo <[email protected]> 2023-03-21 11:21:07 +0100;
653a4a3 Added explanations for new parsers to the vignette by beacalvo <[email protected]> 2023-03-20 17:32:18 +0100;
6e441dd Implemented atena parser method for processing RepeatMasker annotations by beacalvo <[email protected]> 2023-03-14 21:21:50 +0100;
42a8e4d Improved accuracy of fuzzy option of OCTFTA parser by beacalvo <[email protected]> 2023-03-14 20:17:44 +0100;
2129d30 Improved fuzzy option in OCTFTA parser by beacalvo <[email protected]> 2023-03-13 19:06:31 +0100;
c6d4a68 Reducing length of functions of OCTFTA parser by beacalvo <[email protected]> 2023-03-13 00:19:04 +0100;
31ac1c7 Reducing length of functions from OCTFTA annotation parser by beacalvo <[email protected]> 2023-03-10 17:25:39 +0100;
7eb5ae7 Fixed error in unit test from TEtranscripts quantification method by beacalvo <[email protected]> 2023-03-07 23:57:49 +0100;
1156f20 Implemented OneCodeToFindThemAll annotation parser, plus specific function getters for TE classes by beacalvo <[email protected]> 2023-03-07 23:47:16 +0100;
c41a0fb (origin/RELEASE_3_16, RELEASE_3_16) version bump in release by beacalvo <[email protected]> 2023-02-03 15:18:06 +0100;
31ddaff Fixed bug for not properly paired reads by beacalvo <[email protected]> 2023-02-03 12:26:21 +0100;
dcc479c Fixed bug for not properly paired reads by adding isProperPair=TRUE when fragments=FALSE in all methods, for TEtranscripts isProperPair=TRUE always. Added stop() when 'bfl' is empty. by beacalvo <[email protected]> 2023-02-02 17:18:50 +0100;
09e3c99 version bump in devel by beacalvo <[email protected]> 2023-02-03 12:27:13 +0100;
98db345 Fixed bug for not properly paired reads by beacalvo <[email protected]> 2023-02-03 12:26:21 +0100;
defc1f5 Fixed bug for not properly paired reads by adding isProperPair=TRUE when fragments=FALSE in all methods, for TEtranscripts isProperPair=TRUE always. Added stop() when 'bfl' is empty. by beacalvo <[email protected]> 2023-02-02 17:18:50 +0100;
733f401 Using new EM function in the atena method by beacalvo <[email protected]> 2022-12-14 00:34:39 +0100;
76dc341 Updated package version by beacalvo <[email protected]> 2022-12-02 20:47:06 +0100;
7a348e2 Modified initial values for pi and theta parameters by beacalvo <[email protected]> 2022-12-02 20:25:20 +0100;
b1180cb Implemented approach for atena method to address reads with > 1 alignments overlapping the same feature by beacalvo <[email protected]> 2022-12-02 20:19:43 +0100;
5700031 Fixed error in creating reassignment matrix in the atena method by beacalvo <[email protected]> 2022-11-30 17:13:59 +0100;
d8c8d4f bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <[email protected]> 2022-11-01 11:25:40 -0400;
ee2acff bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by J Wokaty <[email protected]> 2022-11-01 11:25:40 -0400;
3badcf7 Version bump by Robert Castelo <[email protected]> 2022-10-31 16:36:49 +0100;
10ae831 Updated NEWS by beacalvo <[email protected]> 2022-10-31 13:53:12 +0100;
50a1afd Updated NEWS by beacalvo <[email protected]> 2022-10-31 13:49:45 +0100;
e7c851d Adapted annotaTEs() to new RepeatMasker annotations in annotationHub by beacalvo <[email protected]> 2022-10-21 18:56:01 +0200;
70f009f Fixed small error in multi no_feature by beacalvo <[email protected]> 2022-09-11 18:52:06 +0200;
8d6d177 Fixed small error by beacalvo <[email protected]> 2022-09-11 17:46:40 +0200;
56d8e1f Fixed small error by beacalvo <[email protected]> 2022-09-11 17:45:09 +0200;
3efe434 Modified input for correcting for effective length in TEtranscripts by beacalvo <[email protected]> 2022-09-09 10:12:03 +0200;
536a47f Modified ovUnion method. Added method OvIntersectionStrict. by beacalvo <[email protected]> 2022-09-08 19:11:14 +0200;
782dfdc Modified overlapping method Union to address alignments overlapping > 1 feature by beacalvo <[email protected]> 2022-09-08 17:23:20 +0200;
625d5df Removed minimum overlap filter in atena by beacalvo <[email protected]> 2022-09-08 16:57:32 +0200;
fd5d25e Modified AS rescaling method in atena by beacalvo <[email protected]> 2022-09-08 16:48:18 +0200;
d5c8a75 (origin/RELEASE_3_15, RELEASE_3_15) Added zzz.R to 'Collate' field by beacalvo <[email protected]> 2022-09-08 12:59:31 +0200;
d26ca51 Implementing informative priors in atena method by beacalvo <[email protected]> 2022-09-07 09:02:54 +0200;
f6f2add Creation of a 4th expression quantification method: atena by beacalvo <[email protected]> 2022-09-06 17:40:02 +0200;
02f334e Changed coercions to dgCMatrix and lgCMatrix to go via virtual classes to comply with latest updates in Matrix version 1.4-2 by Robert Castelo <[email protected]> 2022-09-06 14:03:11 +0200;
143266a Changed coercions to dgCMatrix and lgCMatrix to go via virtual classes to comply with latest updates in Matrix version 1.4-2 by Robert Castelo <[email protected]> 2022-09-06 14:01:13 +0200;
3f46df0 Changed coercions to dgCMatrix and lgCMatrix to go via virtual classes to comply with latest updates in Matrix version 1.4-2 by Robert Castelo <[email protected]> 2022-09-06 13:48:37 +0200;
09d562d Implemented 'multiple no_feature' method in Telescope by beacalvo <[email protected]> 2022-08-04 19:25:33 +0200;
35198b2 Fixed integer overflow error when using large priors by beacalvo <[email protected]> 2022-07-14 17:59:41 +0200;
8441fba Improved 'choose' reassignment method by beacalvo <[email protected]> 2022-06-14 18:24:59 +0200;
8641a1b Fixed small error in conf method reassignment by beacalvo <[email protected]> 2022-06-13 23:36:43 +0200;
daeb395 Modified average reassignment method by beacalvo <[email protected]> 2022-06-13 21:29:56 +0200;
3f7d320 Improved conf reassignment method from Telescope by beacalvo <[email protected]> 2022-06-13 21:05:14 +0200;
b3c838e Implemented 'choose', 'average' and 'conf' reassignment modes in Telescope by beacalvo <[email protected]> 2022-06-13 11:11:58 +0200;
a550df8 Implemented 'choose', 'average' and 'conf' reassignment modes in Telescope by beacalvo <[email protected]> 2022-06-10 16:01:21 +0200;
120c0ef bump x.y.z version to odd y following creation of RELEASE_3_15 branch by Nitesh Turaga <[email protected]> 2022-04-26 16:18:22 +0000;
80cfcbf bump x.y.z version to even y prior to creation of RELEASE_3_15 branch by Nitesh Turaga <[email protected]> 2022-04-26 16:18:22 +0000;
b937d18 Minor vignette corrections and version bump by Robert Castelo <[email protected]> 2022-04-22 18:05:16 +0200;
6bc0653 Updated NEWS file by beacalvo <[email protected]> 2022-04-21 16:19:19 +0200;
60a8d66 Implemented grouping of TEs based on names before quantifying TEs (like --attribute) in Telescope by beacalvo <[email protected]> 2022-03-22 21:57:31 +0100;
596a339 Modified matrix used for EMstep by beacalvo <[email protected]> 2022-03-22 11:50:24 +0100;
50a13d2 Modified matrix used for EMstep by beacalvo <[email protected]> 2022-03-22 11:11:43 +0100;
06c04fd Modified matrix used for EMstep by beacalvo <[email protected]> 2022-03-22 10:22:42 +0100;
d9875db Implemented approach to adjust counts when multimapping reads have alignments mapping to > 1 TE by beacalvo <[email protected]> 2022-03-21 18:45:09 +0100;
d04663b Implemented more efficient counting of multimapping reads overlapping genes by beacalvo <[email protected]> 2022-03-17 15:51:03 +0100;
b608ebe Implemented more efficient counting of multimapping reads overlapping genes by beacalvo <[email protected]> 2022-03-17 15:41:27 +0100;