Showing : csaw • reset
3
votes
5
replies
417
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 9 months ago by ▴ 10 • written 9 months ago by ▴ 30
2
votes
1
reply
279
views
normOffsets in csaw
csaw
updated 10 months ago by ★ 27k • written 10 months ago by ▴ 720
0
votes
2
replies
250
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 11 months ago by ★ 27k • written 11 months ago by ▴ 30
0
votes
4
replies
365
views
DiffBind or csaw between different transcription factors
DiffBind csaw
updated 13 months ago by ★ 27k • written 13 months ago by ▴ 20
1
vote
3
replies
196
views
csaw differential binding visualization
csaw
updated 16 months ago by ★ 27k • written 16 months ago by ▴ 140
2
votes
1
reply
196
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 19 months ago by ★ 27k • written 19 months ago by ▴ 720
3
votes
1
reply
489
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
23 months ago ATpoint ▴ 720
1
vote
7
replies
437
views
Error while running normOffsets in diffhic
diffhic csaw
updated 24 months ago by ★ 27k • written 24 months ago by • 0
6
votes
2
replies
437
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw software error
updated 2.1 years ago by 25k • written 2.1 years ago by ▴ 10
3
votes
7
replies
1.3k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 2.6 years ago by 33k • written 2.6 years ago by • 0
0
votes
7
replies
467
views
A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
2.7 years ago sorjuelal • 0
0
votes
4
replies
509
views
csaw spike-in normalization
ChIP-seq csaw
updated 2.8 years ago by ★ 27k • written 2.8 years ago by ▴ 260
0
votes
1
reply
388
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
updated 2.9 years ago by ★ 27k • written 2.9 years ago by ▴ 90
1
vote
3
replies
501
views
CSAW ready to use R script
csaw
updated 2.9 years ago by ★ 27k • written 2.9 years ago by ▴ 10
0
votes
1
reply
514
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 2.9 years ago by ★ 27k • written 2.9 years ago by ▴ 20
0
votes
2
replies
383
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 3.0 years ago by ★ 27k • written 3.0 years ago by ★ 2.0k
2
votes
5
replies
533
views
Differential ChIP-seq analysis
diffbind csaw
updated 3.1 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
votes
5
replies
619
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 3.2 years ago by ★ 27k • written 3.2 years ago by • 0
2
votes
2
replies
502
views
csaw: Estimate fragment length
csaw
3.4 years ago nicolas.descostes ▴ 20
0
votes
3
replies
593
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 3.8 years ago by 25k • written 3.8 years ago by • 0
3
votes
7
replies
742
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 3.8 years ago by ★ 27k • written 3.8 years ago by ★ 1.5k
1
vote
2
replies
475
views
the Normalise function in csaw
csaw
3.8 years ago tangj ▴ 10
0
votes
2
replies
594
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 3.9 years ago by ★ 27k • written 3.9 years ago by • 0
2
votes
2
replies
565
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 3.9 years ago by ★ 27k • written 3.9 years ago by ▴ 30
3
votes
3
replies
713
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 3.9 years ago by ★ 27k • written 3.9 years ago by • 0
2
votes
11
replies
1.3k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 4.0 years ago by 7.6k • written 4.0 years ago by • 0
1
vote
2
replies
671
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 4.4 years ago by ★ 27k • written 4.4 years ago by ▴ 100
2
votes
2
replies
523
views
Run windowCounts only on annotated regions?
csaw
updated 4.4 years ago by ★ 27k • written 4.4 years ago by ▴ 30
3
votes
1
reply
1.0k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw limma sva qsmooth edger
updated 4.5 years ago by ★ 27k • written 4.5 years ago by ▴ 60
3
votes
6
replies
966
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 4.5 years ago by ★ 27k • written 4.5 years ago by • 0
3
votes
3
replies
808
views
Use csaw to build matrix for heatmap?
csaw chipseq edger
updated 4.5 years ago by ★ 27k • written 4.5 years ago by • 0
3
votes
4
replies
1000
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 4.6 years ago by ★ 27k • written 4.6 years ago by • 0
3
votes
2
replies
1.3k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 4.8 years ago by ★ 27k • written 4.8 years ago by ▴ 10
2
votes
11
replies
1.0k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
4.8 years ago endrebak85 ▴ 30
2
votes
2
replies
624
views
csaw: removing PCR duplicates using dedup flag
csaw dedup
updated 4.8 years ago by 57k • written 4.8 years ago by • 0
2
votes
1
reply
1.1k
views
csaw with negative controls
csaw
5.1 years ago chriad ▴ 10
5
votes
6
replies
1.1k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
5.2 years ago saadmurtazakhan ▴ 10
1
vote
18
replies
1.9k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 5.2 years ago by ★ 27k • written 5.2 years ago by ▴ 10
1
vote
3
replies
1.3k
views
csaw filterWindows function results in a warning: ("Zero library size detected.")
csaw
updated 5.2 years ago by ★ 27k • written 5.2 years ago by ▴ 10
3
votes
1
reply
719
views
window counts in csaw
csaw counts
updated 5.2 years ago by ★ 27k • written 5.2 years ago by • 0
2
votes
1
reply
618
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 5.2 years ago by ★ 27k • written 5.2 years ago by ▴ 30
1
vote
3
replies
716
views
csaw: dumpPE on multiple bam files.
csaw dumpPE windowCounts
5.7 years ago • updated 5.3 years ago asif.zubair • 0
1
vote
1
reply
476
views
csaw: post clustering description of regions
csaw mergeWindows
updated 5.3 years ago by ★ 27k • written 5.3 years ago by • 0
2
votes
1
reply
539
views
csaw: when not to dedup
csaw dedup
updated 5.3 years ago by ★ 27k • written 5.3 years ago by • 0
3
votes
1
reply
553
views
Detection of methylated regions from MeDIP data using csaw
csaw medip-chip
updated 5.3 years ago by ★ 27k • written 5.3 years ago by • 0
4
votes
1
reply
1.7k
views
csaw - workflow to incorporate input/control samples?
csaw chipseq differential binding analysis
updated 5.3 years ago by ★ 27k • written 5.3 years ago by ▴ 10
2
votes
1
reply
675
views
Strategy for choosing window size and read extension length for csaw?
csaw differential binding analysis bin size
updated 5.3 years ago by ★ 27k • written 5.3 years ago by 7.6k
2
votes
3
replies
743
views
Unexpected reversal in normalization factors from csaw
csaw normalization
updated 5.3 years ago by ★ 27k • written 5.3 years ago by 7.6k
1
vote
1
reply
1.2k
views
Differential binding using csaw
csaw differential binding analysis chipseq differential expression differential gene expression
updated 5.3 years ago by ★ 27k • written 5.3 years ago by ▴ 10
2
votes
2
replies
887
views
CSAW : at which bam files are corresponding “up” regions
csaw up regions bam file gain and loss of enrichment
updated 5.4 years ago by ★ 27k • written 5.4 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: tximeta countsFromAbundance for downstream analysis by Michael Love 33k
The counts will not be closely correlated to the TPM across genes, because the gene length is included in the gene count but not in the TPM…
Answer: DESeq2 - understanding intercept and contrasts by Michael Love 33k
For questions on setting up the statistical design and contrasts, I recommend to consult with a local statistician or someone familiar with…
Answer: Interaction terms and selection of coef in normal and shrunk results by Michael Love 33k
Please see the diagram in the vignette on interactions, but for further questions on setting up the design, I recommend to consult with a l…
Answer: about baseMean in DEseq2 by Michael Love 33k
More information about the columns is here: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#access-…
Answer: DESeq2, what to do when controls are 7 times more abundant than treatments by Michael Love 33k
I generally recommend your option 2 here: filtering out genes unless they are minimally expressed in the lowly sequenced condition. This is…
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