Showing : csaw • reset
0
votes
1
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156
views
Restricting differential binding analysis to only TSS-proximal regions
ChIP csaw
updated 4 weeks ago by ★ 28k • written 4 weeks ago by • 0
1
vote
3
replies
704
views
Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 4 weeks ago by • 0 • written 5 weeks ago by • 0
0
votes
0
replies
716
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
15 months ago jared.andrews07 ▴ 30
0
votes
0
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563
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount csaw paired
20 months ago julie.chevalier • 0
2
votes
4
replies
1.4k
views
Error with regionCounts()
csaw
23 months ago Chris ▴ 20
0
votes
0
replies
626
views
some questions about eliminating efficiency biaes in csaw user's guide
csawUsersGuide csaw
2.0 years ago sashu • 0
3
votes
4
replies
2.5k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
2.2 years ago spg • 0
0
votes
0
replies
653
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
2.2 years ago Bogdan ▴ 670
1
vote
3
replies
2.1k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 15 months ago by • 0 • written 2.8 years ago by • 0
1
vote
2
replies
1.8k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 3.0 years ago by ★ 5.2k • written 3.0 years ago by • 0
0
votes
2
replies
883
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw csawUsersGuide
updated 3.3 years ago by ★ 28k • written 3.3 years ago by • 0
0
votes
1
reply
1.9k
views
[CSAW] Erreur : Negative counts not allowed
csaw
3.4 years ago Nicolas Servant ▴ 260
3
votes
5
replies
3.3k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 4.3 years ago by ▴ 10 • written 4.4 years ago by ▴ 50
2
votes
1
reply
1.5k
views
normOffsets in csaw
csaw
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ★ 4.7k
1
vote
2
replies
1.5k
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 50
0
votes
4
replies
2.2k
views
DiffBind or csaw between different transcription factors
DiffBind csaw
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 20
1
vote
3
replies
1.5k
views
csaw differential binding visualization
csaw
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 140
2
votes
1
reply
1.3k
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ★ 4.7k
3
votes
1
reply
2.1k
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
5.5 years ago ATpoint ★ 4.7k
1
vote
7
replies
2.2k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
6
votes
2
replies
1.9k
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw software error
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 30
3
votes
7
replies
4.8k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
7
replies
1.7k
views
A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
6.3 years ago sorjuelal • 0
0
votes
4
replies
2.0k
views
csaw spike-in normalization
ChIP-seq csaw
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 260
0
votes
1
reply
1.1k
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 170
1
vote
3
replies
1.6k
views
CSAW ready to use R script
csaw
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 10
0
votes
1
reply
1.6k
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 60
0
votes
2
replies
1.3k
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ★ 2.0k
2
votes
5
replies
1.5k
views
Differential ChIP-seq analysis
diffbind csaw
updated 6.7 years ago by ★ 5.2k • written 6.7 years ago by • 0
0
votes
5
replies
1.7k
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 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
2
votes
2
replies
1.3k
views
csaw: Estimate fragment length
csaw
7.0 years ago nicolas.descostes ▴ 20
0
votes
3
replies
1.6k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 7.3 years ago by 25k • written 7.4 years ago by • 0
3
votes
7
replies
2.5k
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ★ 1.5k
1
vote
2
replies
1.2k
views
the Normalise function in csaw
csaw
7.4 years ago tangj ▴ 10
0
votes
2
replies
1.5k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 7.4 years ago by ★ 28k • written 7.5 years ago by • 0
2
votes
2
replies
1.4k
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 40
3
votes
3
replies
1.9k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
3
votes
11
replies
2.7k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 7.6 years ago by ★ 7.9k • written 7.6 years ago by ▴ 10
1
vote
2
replies
1.5k
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 100
2
votes
2
replies
1.2k
views
Run windowCounts only on annotated regions?
csaw
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 40
3
votes
1
reply
1.8k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw limma sva qsmooth edger
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 70
3
votes
6
replies
2.2k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 8.1 years ago by ★ 28k • written 8.1 years ago by • 0
3
votes
3
replies
1.9k
views
Use csaw to build matrix for heatmap?
csaw chipseq edger
updated 8.1 years ago by ★ 28k • written 8.1 years ago by • 0
3
votes
4
replies
2.3k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 8.1 years ago by ★ 28k • written 8.1 years ago by • 0
4
votes
2
replies
2.7k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 8.4 years ago by ★ 28k • written 8.4 years ago by ▴ 20
2
votes
11
replies
2.2k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
8.4 years ago endrebak85 ▴ 40
2
votes
2
replies
1.4k
views
csaw: removing PCR duplicates using dedup flag
csaw dedup
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
2
votes
1
reply
2.1k
views
csaw with negative controls
csaw
8.6 years ago chriad ▴ 10
5
votes
6
replies
2.4k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
8.7 years ago saadmurtazakhan ▴ 10
1
vote
18
replies
3.9k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
Awards • All
Popular Question to Matthew McCormack ▴ 180
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.1k
Popular Question to Marco • 0
Popular Question to Stefano Mangiola ▴ 40
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