Showing : csaw • reset
0
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0
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635
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
13 months ago jared.andrews07 ▴ 30
0
votes
0
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499
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount csaw paired
17 months ago julie.chevalier • 0
2
votes
4
replies
1.3k
views
Error with regionCounts()
csaw
20 months ago Chris ▴ 20
0
votes
0
replies
580
views
some questions about eliminating efficiency biaes in csaw user's guide
csawUsersGuide csaw
22 months ago sashu • 0
3
votes
4
replies
2.3k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
24 months ago • updated 23 months ago spg • 0
0
votes
0
replies
594
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
24 months ago Bogdan ▴ 670
1
vote
3
replies
1.9k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 12 months ago by • 0 • written 2.6 years ago by • 0
1
vote
2
replies
1.6k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by • 0
0
votes
2
replies
827
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw csawUsersGuide
updated 3.1 years ago by ★ 28k • written 3.1 years ago by • 0
0
votes
1
reply
1.8k
views
[CSAW] Erreur : Negative counts not allowed
csaw
3.2 years ago Nicolas Servant ▴ 260
3
votes
5
replies
3.1k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 4.1 years ago by ▴ 10 • written 4.2 years ago by ▴ 50
2
votes
1
reply
1.4k
views
normOffsets in csaw
csaw
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ★ 4.6k
1
vote
2
replies
1.4k
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 50
0
votes
4
replies
2.1k
views
DiffBind or csaw between different transcription factors
DiffBind csaw
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 20
1
vote
3
replies
1.4k
views
csaw differential binding visualization
csaw
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 140
2
votes
1
reply
1.2k
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ★ 4.6k
3
votes
1
reply
2.0k
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
5.3 years ago ATpoint ★ 4.6k
1
vote
7
replies
2.0k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
6
votes
2
replies
1.8k
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw software error
updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 30
3
votes
7
replies
4.5k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
7
replies
1.6k
views
A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
6.0 years ago sorjuelal • 0
0
votes
4
replies
1.8k
views
csaw spike-in normalization
ChIP-seq csaw
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 260
0
votes
1
reply
996
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 170
1
vote
3
replies
1.6k
views
CSAW ready to use R script
csaw
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 60
0
votes
2
replies
1.2k
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ★ 2.0k
2
votes
5
replies
1.4k
views
Differential ChIP-seq analysis
diffbind csaw
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by • 0
0
votes
5
replies
1.6k
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 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
2
votes
2
replies
1.2k
views
csaw: Estimate fragment length
csaw
6.8 years ago nicolas.descostes ▴ 20
0
votes
3
replies
1.5k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 7.1 years ago by 25k • written 7.1 years ago by • 0
3
votes
7
replies
2.4k
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ★ 1.5k
1
vote
2
replies
1.1k
views
the Normalise function in csaw
csaw
7.2 years ago tangj ▴ 10
0
votes
2
replies
1.4k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 7.2 years ago by ★ 28k • written 7.2 years ago by • 0
2
votes
2
replies
1.3k
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 40
3
votes
3
replies
1.8k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
3
votes
11
replies
2.6k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 7.4 years ago by ★ 7.9k • written 7.4 years ago by ▴ 10
1
vote
2
replies
1.4k
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 100
2
votes
2
replies
1.1k
views
Run windowCounts only on annotated regions?
csaw
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 40
3
votes
1
reply
1.7k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw limma sva qsmooth edger
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 70
3
votes
6
replies
2.1k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
3
votes
3
replies
1.8k
views
Use csaw to build matrix for heatmap?
csaw chipseq edger
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
3
votes
4
replies
2.2k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
4
votes
2
replies
2.6k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 20
2
votes
11
replies
2.1k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
8.2 years ago endrebak85 ▴ 40
2
votes
2
replies
1.3k
views
csaw: removing PCR duplicates using dedup flag
csaw dedup
updated 8.2 years ago by 67k • written 8.2 years ago by • 0
2
votes
1
reply
2.1k
views
csaw with negative controls
csaw
8.4 years ago chriad ▴ 10
5
votes
6
replies
2.2k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
8.5 years ago saadmurtazakhan ▴ 10
1
vote
18
replies
3.7k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 10
1
vote
3
replies
2.0k
views
csaw filterWindows function results in a warning: ("Zero library size detected.")
csaw
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 10
3
votes
1
reply
1.5k
views
window counts in csaw
csaw counts
updated 8.6 years ago by ★ 28k • written 8.6 years ago by • 0
50 results • Page 1 of 1
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Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi Gordon, Sorry, I didn't see the added response to your original answer. I think that would be a great idea; a novel junction to annot…
Comment: Cannot install GO.db and org.Hs.eg.db by Gabriel • 0
The downloaded source packages are in 'C:Users\gabri\AppData\Local\Temp\RtmpailNer\downloaded_packages' Installation paths not writeable, …
Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi Gordon, Thank you for pointing out that FeatureCounts detects junction reads de novo. It is not in the manual, and maybe could be. Give…
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2 by Michael Love 43k
I've seen in some papers ~1 TPM for saying something in mouse/human etc. was "minimally expressed". For an average length gene, 10 count…
Answer: Feature Counts - potential bug with outfile.jcounts by Gordon Smyth 52k
The behavior that you have documented is expected and is explained in the featureCounts documentation. The first thing to understand is th…
Votes
Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
A: Relations used in GO.db GOBPANCESTOR
Relations used in GO.db GOBPANCESTOR
Answer: RSubread output significantly different from bash Subread output
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