Showing : csaw • reset
6
votes
2
replies
1.5k
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw software error
updated 4.9 years ago by 25k • written 4.9 years ago by ▴ 30
6
votes
2
replies
1.3k
views
Saving the CSAW results to file
edger csaw
updated 8.4 years ago by ★ 28k • written 8.4 years ago by ▴ 30
5
votes
6
replies
2.0k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
7.9 years ago saadmurtazakhan ▴ 10
4
votes
4
replies
1.6k
views
Strand-aware CSAW analysis
csaw chip-seq clip-seq
9.3 years ago • updated 9.2 years ago IV ▴ 30
4
votes
1
reply
2.8k
views
csaw - workflow to incorporate input/control samples?
csaw chipseq differential binding analysis
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 10
4
votes
2
replies
1.4k
views
Csaw : filter windows based on matched negative control
csaw differential binding analysis
8.6 years ago Pierre-François Roux • 0
4
votes
2
replies
2.3k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 20
3
votes
4
replies
1.6k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
17 months ago • updated 16 months ago spg • 0
3
votes
7
replies
2.0k
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ★ 1.5k
3
votes
5
replies
2.5k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 3.5 years ago by ▴ 10 • written 3.6 years ago by ▴ 50
3
votes
1
reply
1.6k
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
4.7 years ago ATpoint ★ 4.1k
3
votes
7
replies
3.8k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 5.4 years ago by 42k • written 5.4 years ago by • 0
3
votes
2
replies
3.5k
views
TMM normalisation method
Csaw csaw
9.1 years ago sergio.espeso-gil • 0
3
votes
1
reply
892
views
Detection of methylated regions from MeDIP data using csaw
csaw medip-chip
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
3
votes
2
replies
1.1k
views
csaw: when not to dedup
csaw dedup
updated 2.7 years ago by • 0 • written 8.0 years ago by • 0
3
votes
1
reply
1.4k
views
window counts in csaw
csaw counts
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
3
votes
4
replies
1.9k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
3
votes
3
replies
1.6k
views
Use csaw to build matrix for heatmap?
csaw chipseq edger
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
3
votes
6
replies
1.9k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
3
votes
1
reply
1.6k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw limma sva qsmooth edger
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 70
3
votes
11
replies
2.3k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 6.8 years ago by ★ 7.9k • written 6.8 years ago by ▴ 10
3
votes
3
replies
1.6k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
2
votes
1
reply
1.0k
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 40
2
votes
1
reply
679
views
csaw not up to date
csaw
updated 8.5 years ago by ★ 28k • written 8.5 years ago by • 0
2
votes
3
replies
946
views
CSAW: getBestTest p-value
csaw
updated 8.6 years ago by 50k • written 8.6 years ago by • 0
2
votes
1
reply
1.2k
views
normOffsets in csaw
csaw
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ★ 4.1k
2
votes
2
replies
1.1k
views
csaw: Estimate fragment length
csaw
6.2 years ago nicolas.descostes ▴ 20
2
votes
1
reply
1.9k
views
csaw with negative controls
csaw
7.8 years ago chriad ▴ 10
2
votes
11
replies
1.9k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
7.6 years ago endrebak85 ▴ 40
2
votes
2
replies
1.1k
views
csaw: removing PCR duplicates using dedup flag
csaw dedup
updated 7.6 years ago by 65k • written 7.6 years ago by • 0
2
votes
4
replies
928
views
Error with regionCounts()
csaw
13 months ago Chris • 0
2
votes
1
reply
947
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ★ 4.1k
2
votes
2
replies
1.3k
views
CSAW : at which bam files are corresponding “up” regions
csaw up regions bam file gain and loss of enrichment
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 10
2
votes
7
replies
1.5k
views
CSAW: GAIN and LOSS of enrichment
csaw
updated 8.1 years ago by ▴ 10 • written 9.0 years ago by • 0
2
votes
3
replies
1.2k
views
Unexpected reversal in normalization factors from csaw
csaw normalization
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ★ 7.9k
2
votes
1
reply
1.3k
views
Strategy for choosing window size and read extension length for csaw?
csaw differential binding analysis bin size
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ★ 7.9k
2
votes
5
replies
1.2k
views
Differential ChIP-seq analysis
diffbind csaw
updated 5.8 years ago by ★ 5.2k • written 5.8 years ago by • 0
2
votes
2
replies
1.1k
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 40
2
votes
2
replies
937
views
Run windowCounts only on annotated regions?
csaw
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 40
2
votes
7
replies
1.3k
views
CSAW: Annotation through clustering with external information
csaw
updated 8.7 years ago by 50k • written 8.7 years ago by • 0
1
vote
2
replies
1.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.1 years ago by ★ 5.2k • written 2.1 years ago by • 0
1
vote
7
replies
1.2k
views
CSAW: filtering prior information
csaw
8.9 years ago sergio.espeso-gil • 0
1
vote
1
reply
958
views
csaw: input coverage RleLists instead of bam files
csaw
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 20
1
vote
1
reply
1.1k
views
FDR calculation by combineTests in csaw
csaw
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 20
1
vote
3
replies
1.1k
views
csaw: dumpPE on multiple bam files.
csaw dumpPE windowCounts
8.5 years ago • updated 8.0 years ago asif.zubair • 0
1
vote
1
reply
1.6k
views
Differential binding using csaw
csaw differential binding analysis chipseq differential expression differential gene expression
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 10
1
vote
1
reply
873
views
csaw: post clustering description of regions
csaw mergeWindows
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
1
vote
3
replies
1.9k
views
csaw filterWindows function results in a warning: ("Zero library size detected.")
csaw
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 10
1
vote
18
replies
3.2k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 10
1
vote
2
replies
1.2k
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 100
50 results • Page 1 of 1
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Comment: EGSEA usage with microarray data (with vooma)? by Chris • 0
Hi Pekka, I also try EGSEA with microarray data. However, I got this error. Would you please have a suggestion? gsa = egsea.ma(numeric…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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