Showing : csaw • reset
0
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0
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333
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
5 months ago jared.andrews07 ▴ 30
0
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0
replies
342
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount csaw paired
10 months ago julie.chevalier • 0
2
votes
4
replies
923
views
Error with regionCounts()
csaw
13 months ago Chris • 0
0
votes
0
replies
413
views
some questions about eliminating efficiency biaes in csaw user's guide
csawUsersGuide csaw
14 months ago sashu • 0
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
16 months ago spg • 0
0
votes
0
replies
452
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normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
16 months ago Bogdan ▴ 670
1
vote
3
replies
1.6k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 5 months ago by • 0 • written 2.0 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
0
votes
2
replies
665
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw csawUsersGuide
updated 2.5 years ago by ★ 28k • written 2.5 years ago by • 0
0
votes
1
reply
1.5k
views
[CSAW] Erreur : Negative counts not allowed
csaw
2.6 years ago Nicolas Servant ▴ 260
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
2
votes
1
reply
1.2k
views
normOffsets in csaw
csaw
updated 3.6 years ago by ★ 28k • written 3.6 years ago by ★ 4.1k
1
vote
2
replies
1.2k
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 50
0
votes
4
replies
1.7k
views
DiffBind or csaw between different transcription factors
DiffBind csaw
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 20
1
vote
3
replies
1.1k
views
csaw differential binding visualization
csaw
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 140
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
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
1
vote
7
replies
1.7k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
6
votes
2
replies
1.5k
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw software error
updated 4.8 years ago by 25k • written 4.8 years ago by ▴ 30
3
votes
7
replies
3.7k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 5.4 years ago by 41k • written 5.4 years ago by • 0
0
votes
7
replies
1.3k
views
A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
5.4 years ago sorjuelal • 0
0
votes
4
replies
1.4k
views
csaw spike-in normalization
ChIP-seq csaw
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 260
0
votes
1
reply
862
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 110
1
vote
3
replies
1.3k
views
CSAW ready to use R script
csaw
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 60
0
votes
2
replies
991
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ★ 2.0k
2
votes
5
replies
1.1k
views
Differential ChIP-seq analysis
diffbind csaw
updated 5.8 years ago by ★ 5.2k • written 5.8 years ago by • 0
0
votes
5
replies
1.4k
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 5.9 years ago by ★ 28k • written 6.0 years ago by • 0
2
votes
2
replies
1.1k
views
csaw: Estimate fragment length
csaw
6.2 years ago nicolas.descostes ▴ 20
0
votes
3
replies
1.3k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 6.5 years ago by 25k • written 6.5 years ago by • 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
1
vote
2
replies
993
views
the Normalise function in csaw
csaw
6.6 years ago tangj ▴ 10
0
votes
2
replies
1.2k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 6.6 years ago by ★ 28k • written 6.6 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
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
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
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
2
votes
2
replies
936
views
Run windowCounts only on annotated regions?
csaw
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 40
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
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
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
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
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
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
1
reply
1.9k
views
csaw with negative controls
csaw
7.8 years ago chriad ▴ 10
5
votes
6
replies
2.0k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
7.9 years ago saadmurtazakhan ▴ 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
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
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
50 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
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Comment: Too many significant genes when integrating gtex and tcga
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