Showing : csaw • reset
3
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5
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186
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csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
3 months ago alexandre.blais • 20 • updated 12 weeks ago Antonio Ahn • 10
2
Votes
1
Reply
136
Views
normOffsets in csaw
csaw
4 months ago ATpoint • 390 • updated 4 months ago Aaron Lun ♦ 26k
0
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2
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104
Views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
4 months ago RichardJActon • 30 • updated 4 months ago Aaron Lun ♦ 26k
0
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4
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193
Views
DiffBind or csaw between different transcription factors
DiffBind csaw
7 months ago GFM • 20 • updated 7 months ago Aaron Lun ♦ 26k
1
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3
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74
Views
csaw differential binding visualization
csaw
9 months ago C T • 140 • updated 9 months ago Aaron Lun ♦ 26k
2
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1
Reply
116
Views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
13 months ago ATpoint • 390 • updated 13 months ago Aaron Lun ♦ 26k
2
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1
Reply
318
Views
Correct use of TMM / normalization factors based on large bins
csaw TMM
17 months ago ATpoint • 390
1
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7
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247
Views
Error while running normOffsets in diffhic
diffhic csaw
17 months ago shopnil99 • 0 • updated 17 months ago Aaron Lun ♦ 26k
6
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2
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291
Views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw software error
18 months ago vanbelj • 10 • updated 18 months ago Martin Morgan 25k
3
Votes
7
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972
Views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
2.1 years ago Yonatan Amzaleg • 0 • updated 2.1 years ago Michael Love 31k
0
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7
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314
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A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
2.2 years ago sorjuelal • 0
0
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4
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384
Views
csaw spike-in normalization
ChIP-seq csaw
2.2 years ago Nicolas Servant • 260 • updated 2.2 years ago Aaron Lun ♦ 26k
0
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1
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292
Views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
2.4 years ago gabriel.hoffman • 90 • updated 2.4 years ago Aaron Lun ♦ 26k
1
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3
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403
Views
CSAW ready to use R script
csaw
2.4 years ago polaxgr • 10 • updated 2.4 years ago Aaron Lun ♦ 26k
0
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1
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438
Views
Best csaw normalization approach for ATAC-seq data
csaw
2.4 years ago Lucy • 0 • updated 2.4 years ago Aaron Lun ♦ 26k
0
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2
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309
Views
csaw: how to hack filtering windows by negative input controls?
csaw
2.5 years ago Jenny Drnevich ♦ 2.0k • updated 2.5 years ago Aaron Lun ♦ 26k
2
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5
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404
Views
Differential ChIP-seq analysis
diffbind csaw
2.6 years ago bioinfo • 0 • updated 2.6 years ago Rory Stark ♦ 3.5k
0
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5
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523
Views
CSAW Spike In Normalization: Error in .local(object, ...) : library sizes of 'se.out' and 'object' are not identical
csaw software error R chip-seq bioconductor
2.7 years ago 94133 • 0 • updated 2.7 years ago Aaron Lun ♦ 26k
2
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2
Replies
411
Views
csaw: Estimate fragment length
csaw
2.9 years ago nicolas.descostes • 20
0
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3
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501
Views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
3.2 years ago favorov • 0 • updated 3.2 years ago Martin Morgan 25k
3
Votes
7
Replies
602
Views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
3.3 years ago Assa Yeroslaviz ♦ 1.5k • updated 3.3 years ago Aaron Lun ♦ 26k
1
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2
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416
Views
the Normalise function in csaw
csaw
3.3 years ago tangj • 10
0
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2
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517
Views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
3.3 years ago gil.hornung • 0 • updated 3.3 years ago Aaron Lun ♦ 26k
2
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2
Replies
456
Views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
3.3 years ago endrebak85 • 30 • updated 3.3 years ago Aaron Lun ♦ 26k
3
Votes
3
Replies
629
Views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
3.4 years ago zhangly811 • 0 • updated 3.4 years ago Aaron Lun ♦ 26k
2
Votes
11
Replies
1.1k
Views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
3.5 years ago jms1223 • 0 • updated 3.5 years ago Ryan C. Thompson 7.6k
1
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2
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594
Views
csaw : effect of library size on filtering of uninteresting windows
csaw
3.8 years ago Vivek.b • 100 • updated 3.8 years ago Aaron Lun ♦ 26k
2
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2
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451
Views
Run windowCounts only on annotated regions?
csaw
3.9 years ago endrebak85 • 30 • updated 3.9 years ago Aaron Lun ♦ 26k
3
Votes
1
Reply
952
Views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw limma sva qsmooth edger
4.0 years ago jma1991 • 40 • updated 4.0 years ago Aaron Lun ♦ 26k
3
Votes
6
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861
Views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
4.0 years ago dalerr • 0 • updated 4.0 years ago Aaron Lun ♦ 26k
3
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3
Replies
695
Views
Use csaw to build matrix for heatmap?
csaw chipseq edger
4.0 years ago jmKeith • 0 • updated 4.0 years ago Aaron Lun ♦ 26k
3
Votes
4
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870
Views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
4.0 years ago siklenkak • 0 • updated 4.0 years ago Aaron Lun ♦ 26k
3
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2
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1.1k
Views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
4.3 years ago s1437643 • 10 • updated 4.3 years ago Aaron Lun ♦ 26k
2
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11
Replies
880
Views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
4.3 years ago endrebak85 • 30
2
Votes
2
Replies
538
Views
csaw: removing PCR duplicates using dedup flag
csaw dedup
4.3 years ago asif.zubair • 0 • updated 4.3 years ago James W. MacDonald 56k
2
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1
Reply
945
Views
csaw with negative controls
csaw
4.5 years ago chriad • 10
5
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6
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889
Views
Getting normalized read counts from region counts
regionCounts TMM csaw
4.6 years ago saadmurtazakhan • 10
1
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18
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1.7k
Views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
4.6 years ago saadmurtazakhan • 10 • updated 4.6 years ago Aaron Lun ♦ 26k
1
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3
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1.1k
Views
csaw filterWindows function results in a warning: ("Zero library size detected.")
csaw
4.7 years ago chriad • 10 • updated 4.7 years ago Aaron Lun ♦ 26k
3
Votes
1
Reply
638
Views
window counts in csaw
csaw counts
4.7 years ago nobishvarghese • 0 • updated 4.7 years ago Aaron Lun ♦ 26k
2
Votes
1
Reply
559
Views
How does csaw handle multiply aligned reads?
csaw chip-seq
4.7 years ago endrebak85 • 30 • updated 4.7 years ago Aaron Lun ♦ 26k
1
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3
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645
Views
csaw: dumpPE on multiple bam files.
csaw dumpPE windowCounts
5.2 years ago • updated 4.7 years ago asif.zubair • 0
1
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1
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429
Views
csaw: post clustering description of regions
csaw mergeWindows
4.7 years ago asif.zubair • 0 • updated 4.7 years ago Aaron Lun ♦ 26k
2
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1
Reply
466
Views
csaw: when not to dedup
csaw dedup
4.7 years ago asif.zubair • 0 • updated 4.7 years ago Aaron Lun ♦ 26k
3
Votes
1
Reply
469
Views
Detection of methylated regions from MeDIP data using csaw
csaw medip-chip
4.7 years ago nobishvarghese • 0 • updated 4.7 years ago Aaron Lun ♦ 26k
4
Votes
1
Reply
1.6k
Views
csaw - workflow to incorporate input/control samples?
csaw chipseq differential binding analysis
4.7 years ago markus.ringner • 10 • updated 4.7 years ago Aaron Lun ♦ 26k
2
Votes
1
Reply
597
Views
Strategy for choosing window size and read extension length for csaw?
csaw differential binding analysis bin size
4.7 years ago Ryan C. Thompson 7.6k • updated 4.7 years ago Aaron Lun ♦ 26k
2
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3
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685
Views
Unexpected reversal in normalization factors from csaw
csaw normalization
4.8 years ago Ryan C. Thompson 7.6k • updated 4.8 years ago Aaron Lun ♦ 26k
1
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1
Reply
979
Views
Differential binding using csaw
csaw differential binding analysis chipseq differential expression differential gene expression