Anders2013: Revision history

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curprev 10:5210:52, 24 February 2024‎ Brb talk contribs‎ 151,501 bytes +89‎ →‎results(contrast)

curprev 21:0621:06, 28 January 2024‎ Brb talk contribs‎ 151,412 bytes +138‎ →‎DESeq2, edgeR, limma

curprev 21:1721:17, 22 August 2023‎ Brb talk contribs‎ 151,274 bytes +140‎ →‎Comparison

curprev 09:4409:44, 9 August 2023‎ Brb talk contribs‎ 151,134 bytes +29‎ →‎recount3
curprev 09:4409:44, 9 August 2023‎ Brb talk contribs‎ 151,105 bytes +129‎ →‎recount2
curprev 09:4209:42, 9 August 2023‎ Brb talk contribs‎ 150,976 bytes +169‎ →‎Comparison

curprev 13:0713:07, 27 July 2023‎ Brb talk contribs‎ 150,807 bytes +350‎ →‎betaPrior is FALSE by default

curprev 16:3916:39, 19 July 2023‎ Brb talk contribs‎ 150,457 bytes +128‎ →‎estimateDispersions()
curprev 10:2910:29, 19 July 2023‎ Brb talk contribs‎ 150,329 bytes +102‎ →‎DESeq2 for DE analysis

curprev 12:0012:00, 7 June 2023‎ Brb talk contribs‎ 150,227 bytes +321‎ →‎Massive Mining of Publicly Available RNA-seq Data from Human and Mouse

curprev 15:0415:04, 21 May 2023‎ Brb talk contribs‎ 149,906 bytes +95‎ →‎collapseReplicates

curprev 14:3114:31, 9 May 2023‎ Brb talk contribs‎ 149,811 bytes +327‎ →‎DESeq() and gene filtering

curprev 21:5921:59, 29 April 2023‎ Brb talk contribs‎ 149,484 bytes +85‎ →‎Values returned from results()

curprev 10:4310:43, 28 April 2023‎ Brb talk contribs‎ 149,399 bytes +448‎ →‎Normalized counts = counts/sizeFactor

curprev 12:4612:46, 16 April 2023‎ Brb talk contribs‎ 148,951 bytes +228‎ →‎Values returned from results()
curprev 12:4312:43, 16 April 2023‎ Brb talk contribs‎ 148,723 bytes +411‎ →‎DESeq2 paired multifactor test

curprev 19:5719:57, 11 April 2023‎ Brb talk contribs‎ 148,312 bytes +319‎ →‎Normalized counts = counts/sizeFactor

curprev 16:2116:21, 30 March 2023‎ Brb talk contribs‎ 147,993 bytes +154‎ →‎DESeq() and gene filtering

curprev 13:5513:55, 11 April 2022‎ Brb talk contribs‎ 147,839 bytes +133‎ →‎rtracklayer package
curprev 13:5313:53, 11 April 2022‎ Brb talk contribs‎ 147,706 bytes +18‎ →‎R

curprev 17:1917:19, 16 February 2022‎ Brb talk contribs‎ 147,688 bytes +575‎ →‎Comparison

curprev 12:5712:57, 29 December 2021‎ Brb talk contribs‎ 147,113 bytes −106‎ →‎sam/bam, "samtools view" and Rsamtools Tags: mobile edit mobile web edit advanced mobile edit
curprev 10:1810:18, 29 December 2021‎ Brb talk contribs‎ 147,219 bytes +429‎ →‎results(contrast)

curprev 17:4117:41, 22 December 2021‎ Brb talk contribs‎ 146,138 bytes +91‎ →‎collapseReplicates

curprev 10:2710:27, 19 December 2021‎ Brb talk contribs‎ 146,047 bytes +329‎ →‎Source code

curprev 16:0516:05, 12 December 2021‎ Brb talk contribs‎ 145,718 bytes +138‎ →‎results(contrast)
curprev 12:4412:44, 12 December 2021‎ Brb talk contribs‎ 145,580 bytes +12‎ →‎Normalized counts = counts/sizeFactor

curprev 16:4016:40, 24 November 2021‎ Brb talk contribs‎ 141,485 bytes +1,280‎ →‎Splice junction
curprev 11:0711:07, 24 November 2021‎ Brb talk contribs‎ 140,205 bytes +675‎ →‎gff/gtf

curprev 17:1617:16, 29 October 2021‎ Brb talk contribs‎ 139,530 bytes 0‎ →‎Pipeline
curprev 17:1417:14, 29 October 2021‎ Brb talk contribs‎ 139,530 bytes +158‎ →‎Error with DESeq2
curprev 08:1708:17, 29 October 2021‎ Brb talk contribs‎ 139,372 bytes +1,723‎ →‎DESeq2 for DE analysis

curprev 21:2621:26, 9 September 2021‎ Brb talk contribs‎ 137,649 bytes +383‎ →‎Normalized counts = counts/sizeFactor
curprev 09:1909:19, 9 September 2021‎ Brb talk contribs‎ 137,266 bytes +168‎ →‎DESeq2 normalization

curprev 13:0513:05, 2 September 2021‎ Brb talk contribs‎ 137,098 bytes +115‎ →‎Comparison

curprev 10:5310:53, 3 July 2021‎ Brb talk contribs‎ 136,983 bytes +234‎ →‎Comparison

curprev 09:2909:29, 24 June 2021‎ Brb talk contribs‎ 136,749 bytes +184‎ →‎Source code

curprev 11:1211:12, 9 March 2021‎ Brb talk contribs‎ 136,565 bytes +226‎ →‎Convert SRA to FASTQ (sra -> fastq)

curprev 11:3311:33, 7 July 2020‎ Brb talk contribs‎ 136,339 bytes +1,195‎ →‎DESeq2 for DE analysis

curprev 10:0610:06, 5 July 2020‎ Brb talk contribs‎ 135,144 bytes +198‎ →‎DESeq2 for DE analysis

curprev 12:3312:33, 3 July 2020‎ Brb talk contribs‎ 134,946 bytes +106‎ →‎estimateSizeFactorsForMatrix()
curprev 11:0511:05, 3 July 2020‎ Brb talk contribs‎ 134,840 bytes +51‎ →‎Source code
curprev 10:5910:59, 3 July 2020‎ Brb talk contribs‎ 134,789 bytes +508‎ →‎estimateSizeFactorsForMatrix()
curprev 10:4510:45, 3 July 2020‎ Brb talk contribs‎ 134,281 bytes +237‎ →‎Normalization-based vs log-ratio transformation-based methods

curprev 21:5321:53, 2 July 2020‎ Brb talk contribs‎ 134,044 bytes +99‎ →‎Negative binomial regression for count data

curprev 21:4421:44, 21 June 2020‎ Brb talk contribs‎ 133,945 bytes +26‎ →‎TCGA/The Cancer Genome Atlas
curprev 21:4421:44, 21 June 2020‎ Brb talk contribs‎ 133,919 bytes +1,100‎ →‎TCGA/The Cancer Genome Atlas
curprev 21:1321:13, 21 June 2020‎ Brb talk contribs‎ 132,819 bytes +1,810‎ →‎TCGA/The Cancer Genome Atlas

curprev 18:1318:13, 9 February 2020‎ Brb talk contribs‎ 131,009 bytes +62‎ →‎Source code
curprev 17:5217:52, 9 February 2020‎ Brb talk contribs‎ 130,947 bytes +126‎ →‎DESeq2 normalization
curprev 17:5117:51, 9 February 2020‎ Brb talk contribs‎ 130,821 bytes +326‎ →‎Source code
curprev 17:2417:24, 9 February 2020‎ Brb talk contribs‎ 130,495 bytes +675‎ →‎DESeq2 normalization

curprev 22:3122:31, 5 February 2020‎ Brb talk contribs‎ 129,820 bytes +150‎ →‎gff/gtf

curprev 10:1310:13, 20 February 2019‎ Brb talk contribs‎ 129,670 bytes +175‎ →‎Convert SRA to FASTQ (sra -> fastq)

curprev 13:5013:50, 7 February 2019‎ Brb talk contribs‎ 129,495 bytes +264‎ →‎ReadCounter - htseq alternative
curprev 12:5212:52, 7 February 2019‎ Brb talk contribs‎ 129,231 bytes +119‎ No edit summary

curprev 14:5114:51, 9 October 2018‎ Brb talk contribs‎ 129,112 bytes +87‎ →‎bed

curprev 12:3712:37, 8 August 2018‎ Brb talk contribs‎ 129,025 bytes +308‎ →‎SRA

curprev 21:1021:10, 24 July 2018‎ Brb talk contribs‎ 128,717 bytes +280‎ →‎DESeq2 normalization

curprev 14:5614:56, 19 January 2018‎ Brb talk contribs‎ 128,437 bytes +316‎ →‎Read quality issues

curprev 12:3012:30, 18 January 2018‎ Brb talk contribs‎ 128,121 bytes +84‎ →‎chromosome names

curprev 12:3112:31, 15 December 2017‎ Brb talk contribs‎ 128,037 bytes +40‎ →‎GATK

curprev 15:4115:41, 17 October 2017‎ Brb talk contribs‎ 127,997 bytes +83‎ →‎Other alignment methods
curprev 13:1513:15, 17 October 2017‎ Brb talk contribs‎ 127,914 bytes +34‎ →‎chromosome sizes
curprev 13:1213:12, 17 October 2017‎ Brb talk contribs‎ 127,880 bytes +716‎ →‎chromosome sizes

curprev 13:5813:58, 30 September 2017‎ Brb talk contribs‎ 127,164 bytes +183‎ →‎Misc

curprev 15:5215:52, 25 September 2017‎ Brb talk contribs‎ 126,981 bytes +363‎ →‎Required tools
curprev 15:2715:27, 25 September 2017‎ Brb talk contribs‎ 126,618 bytes +9‎ →‎Pipeline
curprev 15:2615:26, 25 September 2017‎ Brb talk contribs‎ 126,609 bytes +213‎ →‎Pipeline

curprev 16:0916:09, 15 September 2017‎ Brb talk contribs‎ 126,396 bytes +153‎ →‎Other alignment methods
curprev 08:4408:44, 15 September 2017‎ Brb talk contribs‎ 126,243 bytes +247‎ →‎Other RNA-Seq tools

curprev 10:3510:35, 6 September 2017‎ Brb talk contribs‎ 125,996 bytes +98‎ →‎Reproducible RNA-Seq analysis
curprev 10:3210:32, 6 September 2017‎ Brb talk contribs‎ 125,898 bytes +126‎ →‎What's special with rna-seq count data

curprev 10:3210:32, 21 August 2017‎ Brb talk contribs‎ 125,772 bytes +136‎ →‎IGB

curprev 22:5622:56, 11 August 2017‎ Brb talk contribs‎ 125,636 bytes −1‎ →‎recount2: A multi-experiment resource of analysis-ready RNA-seq gene and exon count datasets
curprev 22:5522:55, 11 August 2017‎ Brb talk contribs‎ 125,637 bytes +132‎ →‎recount2: A multi-experiment resource of analysis-ready RNA-seq gene and exon count datasets

curprev 14:4014:40, 3 August 2017‎ Brb talk contribs‎ 125,505 bytes +180‎ →‎Differential expression analysis
curprev 14:3914:39, 3 August 2017‎ Brb talk contribs‎ 125,325 bytes +220‎ →‎Techniques for characterizing RNA transcripts

curprev 09:5309:53, 2 August 2017‎ Brb talk contribs‎ 125,105 bytes +48‎ →‎qRT-PCR -> Microarray -> Nanostring -> RNA-Seq
curprev 09:5209:52, 2 August 2017‎ Brb talk contribs‎ 125,057 bytes +183‎ →‎Correlation between RNA-Seq and microarrays

curprev 16:2416:24, 27 July 2017‎ Brb talk contribs‎ 124,874 bytes +84‎ →‎recount2
curprev 16:2316:23, 27 July 2017‎ Brb talk contribs‎ 124,790 bytes +63‎ →‎Other RNA-Seq tools

curprev 11:3911:39, 25 July 2017‎ Brb talk contribs‎ 124,727 bytes +164‎ →‎Other RNA-Seq tools
curprev 11:3611:36, 25 July 2017‎ Brb talk contribs‎ 124,563 bytes +188‎ →‎What's special with rna-seq count data

curprev 13:2613:26, 19 July 2017‎ Brb talk contribs‎ 124,375 bytes +217‎ →‎What's special with rna-seq count data

curprev 10:3110:31, 9 June 2017‎ Brb talk contribs‎ 124,158 bytes +58‎ →‎HTSeq
curprev 10:2910:29, 9 June 2017‎ Brb talk contribs‎ 124,100 bytes +745‎ →‎HTSeq

curprev 10:0810:08, 4 June 2017‎ Brb talk contribs‎ 123,355 bytes +163‎ →‎What's special with rna-seq count data

curprev 08:2308:23, 3 June 2017‎ Brb talk contribs‎ 123,192 bytes +79‎ →‎DESeq2 for DE analysis

curprev 15:2715:27, 31 May 2017‎ Brb talk contribs‎ 123,113 bytes +191‎ →‎Overdispersion

curprev 20:4320:43, 30 May 2017‎ Brb talk contribs‎ 122,922 bytes +254‎ →‎Galaxy

curprev 13:1113:11, 10 May 2017‎ Brb talk contribs‎ 122,668 bytes +48‎ →‎Subread
curprev 12:5912:59, 10 May 2017‎ Brb talk contribs‎ 122,620 bytes +44‎ →‎Ion Torrent
curprev 12:5712:57, 10 May 2017‎ Brb talk contribs‎ 122,576 bytes +114‎ →‎Ion Torrent

curprev 08:5308:53, 9 May 2017‎ Brb talk contribs‎ 122,462 bytes −8‎ →‎Power Calculation
curprev 08:4208:42, 9 May 2017‎ Brb talk contribs‎ 122,470 bytes +180‎ →‎Power Calculation

curprev 14:4414:44, 8 May 2017‎ Brb talk contribs‎ 122,290 bytes +161‎ →‎Power Calculation
curprev 14:3814:38, 8 May 2017‎ Brb talk contribs‎ 122,129 bytes +141‎ →‎Power Calculation

curprev 11:0211:02, 16 March 2017‎ Brb talk contribs‎ 117,427 bytes +206‎ →‎GEO

curprev 17:0317:03, 14 March 2017‎ Brb talk contribs‎ 114,987 bytes 0‎ →‎sam/bam, "samtools view" and Rsamtools
curprev 10:2510:25, 14 March 2017‎ Brb talk contribs‎ 114,987 bytes +277‎ →‎fastq

curprev 09:4409:44, 13 March 2017‎ Brb talk contribs‎ 114,710 bytes +845‎ →‎chromosomes
curprev 09:2909:29, 13 March 2017‎ Brb talk contribs‎ 113,865 bytes +483‎ →‎fasta

curprev 14:2314:23, 8 March 2017‎ Brb talk contribs‎ 113,382 bytes +822‎ →‎GSE37704

curprev 16:3316:33, 21 February 2017‎ Brb talk contribs‎ 112,560 bytes +92‎ →‎Galaxy

curprev 16:1216:12, 8 February 2017‎ Brb talk contribs‎ 112,468 bytes +522‎ →‎Performance

curprev 10:4510:45, 31 January 2017‎ Brb talk contribs‎ 111,946 bytes +94‎ →‎GATK

curprev 16:2316:23, 27 January 2017‎ Brb talk contribs‎ 111,852 bytes +9‎ →‎Power Calculation
curprev 16:2216:22, 27 January 2017‎ Brb talk contribs‎ 111,843 bytes +193‎ →‎What's special with rna-seq count data

curprev 15:4315:43, 11 January 2017‎ Brb talk contribs‎ 110,666 bytes +195‎ →‎Normalization

curprev 15:0515:05, 18 December 2016‎ Brb talk contribs‎ 110,471 bytes +70‎ →‎ENCODE

curprev 15:5515:55, 1 December 2016‎ Brb talk contribs‎ 110,401 bytes +123‎ →‎Galaxy
curprev 15:5115:51, 1 December 2016‎ Brb talk contribs‎ 110,278 bytes +88‎ →‎Galaxy

curprev 20:4020:40, 7 October 2016‎ Brb talk contribs‎ 110,190 bytes +183‎ →‎Normalization

curprev 20:0920:09, 10 September 2016‎ Brb talk contribs‎ 110,007 bytes +54‎ →‎sam/bam, "samtools view" and Rsamtools
curprev 20:0620:06, 10 September 2016‎ Brb talk contribs‎ 109,953 bytes +1,895‎ →‎sam/bam, "samtools view" and Rsamtools

curprev 11:1011:10, 8 September 2016‎ Brb talk contribs‎ 108,058 bytes +469‎ →‎Count reads using htseq-count (sam -> count)

curprev 21:1221:12, 3 September 2016‎ Brb talk contribs‎ 107,589 bytes +42‎ →‎sam/bam, "samtools view" and Rsamtools

curprev 14:2214:22, 2 September 2016‎ Brb talk contribs‎ 107,547 bytes +132‎ →‎Remove 'chr' from fasta
curprev 14:2014:20, 2 September 2016‎ Brb talk contribs‎ 107,415 bytes +830‎ →‎chromosomes

curprev 16:0516:05, 1 September 2016‎ Brb talk contribs‎ 106,585 bytes +180‎ →‎chromosomes

curprev 09:0009:00, 31 August 2016‎ Brb talk contribs‎ 106,405 bytes +448‎ →‎GSE64570, GSE69244, GSE72165

curprev 14:0514:05, 25 August 2016‎ Brb talk contribs‎ 105,957 bytes +250‎ →‎sam/bam, "samtools view" and Rsamtools

curprev 16:2716:27, 24 August 2016‎ Brb talk contribs‎ 105,707 bytes +6‎ →‎GATK
curprev 16:2616:26, 24 August 2016‎ Brb talk contribs‎ 105,701 bytes +124‎ →‎GATK

curprev 14:3914:39, 17 August 2016‎ Brb talk contribs‎ 102,352 bytes +13‎ →‎GATK

curprev 16:4916:49, 13 August 2016‎ Brb talk contribs‎ 102,339 bytes +105‎ →‎DESeq2 normalization

curprev 18:3318:33, 12 August 2016‎ Brb talk contribs‎ 102,234 bytes +426‎ →‎DESeq2 normalization
curprev 18:0518:05, 12 August 2016‎ Brb talk contribs‎ 101,808 bytes +388‎ →‎DESeq2 normalization

curprev 14:4914:49, 11 August 2016‎ Brb talk contribs‎ 101,420 bytes +12‎ →‎sam/bam, "samtools view" and Rsamtools
curprev 11:1311:13, 11 August 2016‎ Brb talk contribs‎ 101,408 bytes +89‎ →‎sam/bam, "samtools view" and Rsamtools

curprev 13:2513:25, 8 August 2016‎ Brb talk contribs‎ 100,445 bytes +69‎ →‎sam/bam, "samtools view" and Rsamtools
curprev 13:0913:09, 8 August 2016‎ Brb talk contribs‎ 100,376 bytes +274‎ →‎sam/bam, "samtools view" and Rsamtools
curprev 11:5911:59, 8 August 2016‎ Brb talk contribs‎ 100,102 bytes +31‎ →‎sam/bam, "samtools view" and Rsamtools
curprev 11:5711:57, 8 August 2016‎ Brb talk contribs‎ 100,071 bytes +461‎ →‎sam/bam, "samtools view" and Rsamtools

curprev 08:0908:09, 6 August 2016‎ Brb talk contribs‎ 99,610 bytes +1,531‎ →‎chromosomes

curprev 16:2616:26, 27 July 2016‎ Brb talk contribs‎ 90,450 bytes +267‎ →‎Splice junctions
curprev 13:3513:35, 27 July 2016‎ Brb talk contribs‎ 90,183 bytes +55‎ →‎Small test data from Tophat (paired end)
curprev 13:2113:21, 27 July 2016‎ Brb talk contribs‎ 90,128 bytes −116‎ →‎GSE51403 (full R script)
curprev 13:1713:17, 27 July 2016‎ Brb talk contribs‎ 90,244 bytes +184‎ →‎GEO

curprev 22:0022:00, 25 July 2016‎ Brb talk contribs‎ 90,060 bytes 0‎ →‎[http://www.genefriends.org/ReadCounter ReadCounter= - htseq alternative
curprev 16:3016:30, 25 July 2016‎ Brb talk contribs‎ 90,060 bytes +3,357‎ →‎DESeq for DE analysis

curprev 21:2021:20, 22 July 2016‎ Brb talk contribs‎ 86,703 bytes +156‎ →‎Count reads using htseq-count (sam -> count)
curprev 21:1021:10, 22 July 2016‎ Brb talk contribs‎ 86,547 bytes +227‎ →‎Count reads using htseq-count (sam -> count)

curprev 09:2309:23, 20 July 2016‎ Brb talk contribs‎ 86,320 bytes +569‎ →‎Some lessons

curprev 16:2816:28, 9 March 2016‎ Brb talk contribs‎ 85,393 bytes +346‎ →‎Inspect alignments with IGV

curprev 13:4613:46, 1 March 2016‎ Brb talk contribs‎ 85,047 bytes +39‎ →‎sam/bam, "samtools view" and Rsamtools

curprev 10:1010:10, 26 February 2016‎ Brb talk contribs‎ 85,008 bytes +90‎ →‎chromosomes

curprev 11:2711:27, 25 February 2016‎ Brb talk contribs‎ 84,918 bytes +235‎ →‎fasta

curprev 13:2913:29, 24 February 2016‎ Brb talk contribs‎ 84,683 bytes +20‎ →‎fasta
curprev 13:2713:27, 24 February 2016‎ Brb talk contribs‎ 84,663 bytes +192‎ →‎sam/bam, "samtools view" and Rsamtools
curprev 12:5412:54, 24 February 2016‎ Brb talk contribs‎ 84,471 bytes +458‎ →‎Download reference genome (for Tophat)
curprev 12:3912:39, 24 February 2016‎ Brb talk contribs‎ 84,013 bytes +610‎ →‎sam/bam, "samtools view" and Rsamtools

curprev 20:5420:54, 23 February 2016‎ Brb talk contribs‎ 83,403 bytes +319‎ →‎sam, bam and samtools view
curprev 20:3620:36, 23 February 2016‎ Brb talk contribs‎ 83,084 bytes +265‎ →‎Organize, sort and index the BAM files and create SAM files (bam -> sam)
curprev 20:2820:28, 23 February 2016‎ Brb talk contribs‎ 82,819 bytes +173‎ →‎sam, bam
curprev 12:4312:43, 23 February 2016‎ Brb talk contribs‎ 82,646 bytes +413‎ →‎fasta

curprev 12:3412:34, 15 January 2016‎ Brb talk contribs‎ 82,233 bytes +380‎ →‎TCGA

curprev 14:3514:35, 31 December 2015‎ Brb talk contribs‎ 81,853 bytes +180‎ →‎GEO

curprev 14:2214:22, 7 December 2015‎ Brb talk contribs‎ 81,673 bytes +96‎ →‎GEO

curprev 11:3711:37, 10 November 2015‎ Brb talk contribs‎ 81,577 bytes +81,250‎ No edit summary
curprev 11:3311:33, 10 November 2015‎ Brb talk contribs‎ 327 bytes −80,979‎ Replaced content with "== ReCount == * [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3229291/ ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets] * http://bowtie-b..."

curprev 16:0816:08, 28 October 2015‎ Brb talk contribs‎ 81,306 bytes −143‎ →‎Normalization
curprev 16:0516:05, 28 October 2015‎ Brb talk contribs‎ 81,449 bytes +143‎ →‎Normalization
curprev 16:0116:01, 28 October 2015‎ Brb talk contribs‎ 81,306 bytes +176‎ →‎Normalization

Anders2013: Revision history

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