Showing : csaw • reset
3
votes
5
replies
314
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 6 months ago by ▴ 10 • written 7 months ago by ▴ 30
2
votes
1
reply
209
views
normOffsets in csaw
csaw
updated 8 months ago by ★ 26k • written 8 months ago by ▴ 630
0
votes
2
replies
180
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 8 months ago by ★ 26k • written 8 months ago by ▴ 30
0
votes
4
replies
270
views
DiffBind or csaw between different transcription factors
DiffBind csaw
updated 10 months ago by ★ 26k • written 11 months ago by ▴ 20
1
vote
3
replies
127
views
csaw differential binding visualization
csaw
updated 13 months ago by ★ 26k • written 13 months ago by ▴ 140
2
votes
1
reply
155
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 17 months ago by ★ 26k • written 17 months ago by ▴ 630
2
votes
1
reply
410
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
20 months ago ATpoint ▴ 630
1
vote
7
replies
347
views
Error while running normOffsets in diffhic
diffhic csaw
updated 21 months ago by ★ 26k • written 21 months ago by • 0
6
votes
2
replies
369
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw software error
updated 22 months ago by 25k • written 22 months ago by ▴ 10
3
votes
7
replies
1.1k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 2.4 years ago by 32k • written 2.4 years ago by • 0
0
votes
7
replies
363
views
A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
2.5 years ago sorjuelal • 0
0
votes
4
replies
445
views
csaw spike-in normalization
ChIP-seq csaw
updated 2.5 years ago by ★ 26k • written 2.5 years ago by ▴ 260
0
votes
1
reply
315
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
updated 2.7 years ago by ★ 26k • written 2.7 years ago by ▴ 90
1
vote
3
replies
456
views
CSAW ready to use R script
csaw
updated 2.7 years ago by ★ 26k • written 2.7 years ago by ▴ 10
0
votes
1
reply
479
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 2.7 years ago by ★ 26k • written 2.7 years ago by • 0
0
votes
2
replies
351
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 2.8 years ago by ★ 26k • written 2.8 years ago by ★ 2.0k
2
votes
5
replies
463
views
Differential ChIP-seq analysis
diffbind csaw
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
0
votes
5
replies
574
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
updated 3.0 years ago by ★ 26k • written 3.0 years ago by • 0
2
votes
2
replies
459
views
csaw: Estimate fragment length
csaw
3.2 years ago nicolas.descostes ▴ 20
0
votes
3
replies
544
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 3.5 years ago by 25k • written 3.6 years ago by • 0
3
votes
7
replies
671
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 3.6 years ago by ★ 26k • written 3.6 years ago by ★ 1.5k
1
vote
2
replies
442
views
the Normalise function in csaw
csaw
3.6 years ago tangj ▴ 10
0
votes
2
replies
547
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 3.6 years ago by ★ 26k • written 3.6 years ago by • 0
2
votes
2
replies
500
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 3.7 years ago by ★ 26k • written 3.7 years ago by ▴ 30
3
votes
3
replies
666
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 3.7 years ago by ★ 26k • written 3.7 years ago by • 0
2
votes
11
replies
1.2k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 3.8 years ago by 7.6k • written 3.8 years ago by • 0
1
vote
2
replies
635
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 4.1 years ago by ★ 26k • written 4.1 years ago by ▴ 100
2
votes
2
replies
486
views
Run windowCounts only on annotated regions?
csaw
updated 4.2 years ago by ★ 26k • written 4.2 years ago by ▴ 30
3
votes
1
reply
989
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw limma sva qsmooth edger
updated 4.3 years ago by ★ 26k • written 4.3 years ago by ▴ 60
3
votes
6
replies
913
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 4.3 years ago by ★ 26k • written 4.3 years ago by • 0
3
votes
3
replies
731
views
Use csaw to build matrix for heatmap?
csaw chipseq edger
updated 4.3 years ago by ★ 26k • written 4.3 years ago by • 0
3
votes
4
replies
936
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 4.3 years ago by ★ 26k • written 4.3 years ago by • 0
3
votes
2
replies
1.2k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 4.6 years ago by ★ 26k • written 4.6 years ago by ▴ 10
2
votes
11
replies
949
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
4.6 years ago endrebak85 ▴ 30
2
votes
2
replies
582
views
csaw: removing PCR duplicates using dedup flag
csaw dedup
updated 4.6 years ago by 56k • written 4.6 years ago by • 0
2
votes
1
reply
1.0k
views
csaw with negative controls
csaw
4.8 years ago chriad ▴ 10
5
votes
6
replies
952
views
Getting normalized read counts from region counts
regionCounts TMM csaw
4.9 years ago saadmurtazakhan ▴ 10
1
vote
18
replies
1.8k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 5.0 years ago by ★ 26k • written 5.0 years ago by ▴ 10
1
vote
3
replies
1.2k
views
csaw filterWindows function results in a warning: ("Zero library size detected.")
csaw
updated 5.0 years ago by ★ 26k • written 5.0 years ago by ▴ 10
3
votes
1
reply
685
views
window counts in csaw
csaw counts
updated 5.0 years ago by ★ 26k • written 5.0 years ago by • 0
2
votes
1
reply
589
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 5.0 years ago by ★ 26k • written 5.0 years ago by ▴ 30
1
vote
3
replies
681
views
csaw: dumpPE on multiple bam files.
csaw dumpPE windowCounts
5.5 years ago • updated 5.0 years ago asif.zubair • 0
1
vote
1
reply
452
views
csaw: post clustering description of regions
csaw mergeWindows
updated 5.0 years ago by ★ 26k • written 5.0 years ago by • 0
2
votes
1
reply
493
views
csaw: when not to dedup
csaw dedup
updated 5.0 years ago by ★ 26k • written 5.0 years ago by • 0
3
votes
1
reply
494
views
Detection of methylated regions from MeDIP data using csaw
csaw medip-chip
updated 5.0 years ago by ★ 26k • written 5.0 years ago by • 0
4
votes
1
reply
1.7k
views
csaw - workflow to incorporate input/control samples?
csaw chipseq differential binding analysis
updated 5.0 years ago by ★ 26k • written 5.0 years ago by ▴ 10
2
votes
1
reply
635
views
Strategy for choosing window size and read extension length for csaw?
csaw differential binding analysis bin size
updated 5.1 years ago by ★ 26k • written 5.1 years ago by 7.6k
2
votes
3
replies
715
views
Unexpected reversal in normalization factors from csaw
csaw normalization
updated 5.1 years ago by ★ 26k • written 5.1 years ago by 7.6k
1
vote
1
reply
1.1k
views
Differential binding using csaw
csaw differential binding analysis chipseq differential expression differential gene expression
updated 5.1 years ago by ★ 26k • written 5.1 years ago by ▴ 10
2
votes
2
replies
841
views
CSAW : at which bam files are corresponding “up” regions
csaw up regions bam file gain and loss of enrichment
updated 5.2 years ago by ★ 26k • written 5.2 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: DeSeq2 with 2 conditions and 3 time points by swbarnes2 ▴ 730
> do I need to somehow perform a normalization to baseline If you want to compare two things, just compare two things. Adding in the v…
Answer: could not duplicate the fragment length in "Reads to Regions" csaw tutorial by Aaron Lun ★ 26k
Changes in the mapping proportions aren't surprising, the aligner has probably changed a fair bit in the last 6 years since the paper was p…
Comment: Warning in EnhancedVolcano plot by Kevin Blighe 2.9k
Thanks - that is interesting to know.
Comment: Warning in EnhancedVolcano plot by charles.feigin ▴ 20
Sorry, one more quick reply. So, changing lengthConnectors and/or directionConnectors doesn't let me render any more connectors, but I foun…
Comment: Warning in EnhancedVolcano plot by charles.feigin ▴ 20
Ok I understand. I'll play around with these. Thank you!
Votes
Comment: Warning in EnhancedVolcano plot
Comment: Warning in EnhancedVolcano plot
Comment: Warning in EnhancedVolcano plot
Comment: Warning in EnhancedVolcano plot
A: How to make a (limma) heatmap displaying gene ID's as rownames
Awards • All
Scholar to Aaron Lun ★ 26k
Popular Question to Nik Tuzov ▴ 70
Scholar to James W. MacDonald 56k
Scholar to swbarnes2 ▴ 730
Popular Question to rfes • 0
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