Showing : csaw • reset
1
vote
8
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2.7k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
8 months ago • updated 7 months ago Luca • 0
0
votes
1
reply
407
views
Restricting differential binding analysis to only TSS-proximal regions
ChIP csaw
updated 10 months ago by ★ 29k • written 10 months ago by • 0
1
vote
3
replies
1.2k
views
Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 10 months ago by • 0 • written 10 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
2.1 years ago jared.andrews07 ▴ 30
0
votes
0
replies
710
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount csaw paired
2.4 years ago julie.chevalier • 0
2
votes
4
replies
1.7k
views
Error with regionCounts()
csaw
2.7 years ago Chris ▴ 20
0
votes
0
replies
786
views
some questions about eliminating efficiency biaes in csaw user's guide
csawUsersGuide csaw
2.8 years ago sashu • 0
3
votes
4
replies
3.1k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
3.0 years ago • updated 2.9 years ago spg • 0
0
votes
0
replies
806
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
3.0 years ago Bogdan ▴ 670
1
vote
3
replies
2.5k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 2.0 years ago by • 0 • written 3.6 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 3.7 years ago by ★ 5.2k • written 3.7 years ago by • 0
0
votes
2
replies
1.1k
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw csawUsersGuide
updated 4.1 years ago by ★ 29k • written 4.1 years ago by • 0
0
votes
1
reply
2.1k
views
[CSAW] Erreur : Negative counts not allowed
csaw
4.2 years ago Nicolas Servant ▴ 260
3
votes
5
replies
3.8k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 5.1 years ago by ▴ 10 • written 5.1 years ago by ▴ 50
2
votes
1
reply
1.7k
views
normOffsets in csaw
csaw
updated 5.2 years ago by ★ 29k • written 5.2 years ago by ★ 5.0k
1
vote
2
replies
1.7k
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ▴ 50
0
votes
4
replies
2.5k
views
DiffBind or csaw between different transcription factors
DiffBind csaw
updated 5.5 years ago by ★ 29k • written 5.5 years ago by ▴ 20
1
vote
3
replies
1.8k
views
csaw differential binding visualization
csaw
updated 5.7 years ago by ★ 29k • written 5.7 years ago by ▴ 140
2
votes
1
reply
1.6k
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 6.0 years ago by ★ 29k • written 6.0 years ago by ★ 5.0k
3
votes
1
reply
2.4k
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
6.3 years ago ATpoint ★ 5.0k
1
vote
7
replies
2.5k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 6.3 years ago by ★ 29k • written 6.3 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 6.4 years ago by 25k • written 6.4 years ago by ▴ 30
3
votes
7
replies
5.5k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 7.0 years ago by 43k • written 7.0 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
7.0 years ago sorjuelal • 0
0
votes
4
replies
2.4k
views
csaw spike-in normalization
ChIP-seq csaw
updated 7.1 years ago by ★ 29k • written 7.1 years ago by ▴ 260
0
votes
1
reply
1.2k
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
updated 7.2 years ago by ★ 29k • written 7.2 years ago by ▴ 170
1
vote
3
replies
1.8k
views
CSAW ready to use R script
csaw
updated 7.2 years ago by ★ 29k • written 7.2 years ago by ▴ 10
0
votes
1
reply
1.8k
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 7.3 years ago by ★ 29k • written 7.3 years ago by ▴ 60
0
votes
2
replies
1.5k
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 7.4 years ago by ★ 29k • written 7.4 years ago by ★ 2.0k
2
votes
5
replies
1.8k
views
Differential ChIP-seq analysis
diffbind csaw
updated 7.4 years ago by ★ 5.2k • written 7.4 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 7.5 years ago by ★ 29k • written 7.5 years ago by • 0
2
votes
2
replies
1.5k
views
csaw: Estimate fragment length
csaw
7.7 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 8.1 years ago by 25k • written 8.1 years ago by • 0
3
votes
7
replies
3.0k
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ★ 1.5k
1
vote
2
replies
1.4k
views
the Normalise function in csaw
csaw
8.2 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 8.2 years ago by ★ 29k • written 8.2 years ago by • 0
2
votes
2
replies
1.5k
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 40
3
votes
3
replies
2.2k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 8.2 years ago by ★ 29k • written 8.2 years ago by • 0
3
votes
11
replies
3.2k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 8.4 years ago by ★ 7.9k • written 8.4 years ago by ▴ 10
1
vote
2
replies
1.7k
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 8.7 years ago by ★ 29k • written 8.7 years ago by ▴ 100
2
votes
2
replies
1.3k
views
Run windowCounts only on annotated regions?
csaw
updated 8.8 years ago by ★ 29k • written 8.8 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 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 70
3
votes
6
replies
2.5k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 8.8 years ago by ★ 29k • written 8.8 years ago by • 0
3
votes
3
replies
2.1k
views
Use csaw to build matrix for heatmap?
csaw chipseq edger
updated 8.8 years ago by ★ 29k • written 8.8 years ago by • 0
3
votes
4
replies
2.7k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 8.9 years ago by ★ 29k • written 8.9 years ago by • 0
4
votes
2
replies
3.0k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 9.1 years ago by ★ 29k • written 9.1 years ago by ▴ 20
2
votes
11
replies
2.5k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
9.2 years ago endrebak85 ▴ 40
2
votes
2
replies
1.6k
views
csaw: removing PCR duplicates using dedup flag
csaw dedup
updated 9.2 years ago by 68k • written 9.2 years ago by • 0
2
votes
1
reply
2.3k
views
csaw with negative controls
csaw
9.4 years ago chriad ▴ 10
5
votes
6
replies
2.7k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
9.5 years ago saadmurtazakhan ▴ 10
75 results • Page 1 of 2
Recent ...
Replies
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.2k
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