Showing : Csaw • reset
1
vote
8
replies
2.8k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
10 months ago • updated 9 months ago Luca • 0
0
votes
1
reply
467
views
Restricting differential binding analysis to only TSS-proximal regions
ChIP csaw
updated 11 months ago by ★ 29k • written 11 months ago by • 0
1
vote
3
replies
1.2k
views
Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 11 months ago by • 0 • written 11 months ago by • 0
0
votes
0
replies
1.0k
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
2.2 years ago jared.andrews07 ▴ 30
0
votes
0
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758
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount csaw paired
2.6 years ago julie.chevalier • 0
2
votes
4
replies
1.7k
views
Error with regionCounts()
csaw
2.8 years ago Chris ▴ 20
0
votes
0
replies
808
views
some questions about eliminating efficiency biaes in csaw user's guide
csawUsersGuide csaw
2.9 years ago sashu • 0
3
votes
4
replies
3.2k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
3.1 years ago • updated 3.0 years ago spg • 0
0
votes
0
replies
825
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
3.1 years ago Bogdan ▴ 670
1
vote
3
replies
2.5k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 2.1 years ago by • 0 • written 3.7 years ago by • 0
1
vote
2
replies
2.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 3.8 years ago by ★ 5.2k • written 3.8 years ago by • 0
0
votes
2
replies
1.2k
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw csawUsersGuide
updated 4.2 years ago by ★ 29k • written 4.2 years ago by • 0
0
votes
1
reply
2.1k
views
[CSAW] Erreur : Negative counts not allowed
csaw
4.3 years ago Nicolas Servant ▴ 260
3
votes
5
replies
4.0k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 5.2 years ago by ▴ 10 • written 5.3 years ago by ▴ 50
2
votes
1
reply
1.7k
views
normOffsets in csaw
csaw
updated 5.3 years ago by ★ 29k • written 5.4 years ago by ★ 5.0k
1
vote
2
replies
1.7k
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 50
0
votes
4
replies
2.6k
views
DiffBind or csaw between different transcription factors
DiffBind csaw
updated 5.6 years ago by ★ 29k • written 5.6 years ago by ▴ 20
1
vote
3
replies
1.8k
views
csaw differential binding visualization
csaw
updated 5.8 years ago by ★ 29k • written 5.8 years ago by ▴ 140
2
votes
1
reply
1.7k
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 6.1 years ago by ★ 29k • written 6.1 years ago by ★ 5.0k
3
votes
1
reply
2.5k
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
6.4 years ago ATpoint ★ 5.0k
1
vote
7
replies
2.6k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
6
votes
2
replies
2.1k
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw software error
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 30
3
votes
7
replies
5.7k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
7
replies
2.0k
views
A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
7.1 years ago sorjuelal • 0
0
votes
4
replies
2.4k
views
csaw spike-in normalization
ChIP-seq csaw
updated 7.2 years ago by ★ 29k • written 7.2 years ago by ▴ 260
0
votes
1
reply
1.3k
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
updated 7.4 years ago by ★ 29k • written 7.4 years ago by ▴ 170
1
vote
3
replies
1.9k
views
CSAW ready to use R script
csaw
updated 7.4 years ago by ★ 29k • written 7.4 years ago by ▴ 10
0
votes
1
reply
1.8k
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 7.4 years ago by ★ 29k • written 7.4 years ago by ▴ 60
0
votes
2
replies
1.6k
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 7.5 years ago by ★ 29k • written 7.5 years ago by ★ 2.0k
2
votes
5
replies
1.9k
views
Differential ChIP-seq analysis
diffbind csaw
updated 7.5 years ago by ★ 5.2k • written 7.5 years ago by • 0
0
votes
5
replies
2.0k
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 7.6 years ago by ★ 29k • written 7.7 years ago by • 0
2
votes
2
replies
1.5k
views
csaw: Estimate fragment length
csaw
7.9 years ago nicolas.descostes ▴ 20
0
votes
3
replies
1.8k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 8.2 years ago by 25k • written 8.2 years ago by • 0
3
votes
7
replies
3.1k
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ★ 1.5k
1
vote
2
replies
1.4k
views
the Normalise function in csaw
csaw
8.3 years ago tangj ▴ 10
0
votes
2
replies
1.8k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 8.3 years ago by ★ 29k • written 8.3 years ago by • 0
2
votes
2
replies
1.6k
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 8.3 years ago by ★ 29k • written 8.3 years ago by ▴ 40
3
votes
3
replies
2.3k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 8.4 years ago by ★ 29k • written 8.4 years ago by • 0
3
votes
11
replies
3.3k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 8.5 years ago by ★ 7.9k • written 8.5 years ago by ▴ 10
1
vote
2
replies
1.7k
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 100
2
votes
2
replies
1.3k
views
Run windowCounts only on annotated regions?
csaw
updated 8.9 years ago by ★ 29k • written 8.9 years ago by ▴ 40
3
votes
1
reply
2.0k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw limma sva qsmooth edger
updated 9.0 years ago by ★ 29k • written 9.0 years ago by ▴ 70
3
votes
6
replies
2.6k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 9.0 years ago by ★ 29k • written 9.0 years ago by • 0
3
votes
3
replies
2.2k
views
Use csaw to build matrix for heatmap?
csaw chipseq edger
updated 9.0 years ago by ★ 29k • written 9.0 years ago by • 0
3
votes
4
replies
2.8k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 9.0 years ago by ★ 29k • written 9.0 years ago by • 0
4
votes
2
replies
3.1k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 9.3 years ago by ★ 29k • written 9.3 years ago by ▴ 20
2
votes
11
replies
2.6k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
9.3 years ago endrebak85 ▴ 40
2
votes
2
replies
1.6k
views
csaw: removing PCR duplicates using dedup flag
csaw dedup
updated 9.3 years ago by 68k • written 9.3 years ago by • 0
2
votes
1
reply
2.4k
views
csaw with negative controls
csaw
9.5 years ago chriad ▴ 10
5
votes
6
replies
2.8k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
9.6 years ago saadmurtazakhan ▴ 10
75 results • Page 1 of 2
Recent ...
Replies
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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