Showing : Csaw • reset
1
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8
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
6 weeks ago • updated 17 days ago Luca • 0
0
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1
reply
208
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Restricting differential binding analysis to only TSS-proximal regions
ChIP csaw
updated 12 weeks ago by ★ 28k • written 12 weeks ago by • 0
1
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3
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785
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Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 12 weeks ago by • 0 • written 3 months ago by • 0
0
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0
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769
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
17 months ago jared.andrews07 ▴ 30
0
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0
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594
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Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount csaw paired
22 months ago julie.chevalier • 0
2
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4
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1.4k
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Error with regionCounts()
csaw
2.1 years ago Chris ▴ 20
0
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0
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649
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some questions about eliminating efficiency biaes in csaw user's guide
csawUsersGuide csaw
2.2 years ago sashu • 0
3
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4
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2.6k
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RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
2.4 years ago • updated 2.3 years ago spg • 0
0
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0
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680
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normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
2.4 years ago Bogdan ▴ 670
1
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3
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2.1k
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regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 16 months ago by • 0 • written 3.0 years ago by • 0
1
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2
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1.9k
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Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 3.1 years ago by ★ 5.2k • written 3.1 years ago by • 0
0
votes
2
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914
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw csawUsersGuide
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
0
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1
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2.0k
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[CSAW] Erreur : Negative counts not allowed
csaw
3.5 years ago Nicolas Servant ▴ 260
3
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5
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3.5k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 4.5 years ago by ▴ 10 • written 4.5 years ago by ▴ 50
2
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1
reply
1.5k
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normOffsets in csaw
csaw
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ★ 4.8k
1
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2
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1.5k
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 50
0
votes
4
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2.3k
views
DiffBind or csaw between different transcription factors
DiffBind csaw
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 20
1
vote
3
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1.5k
views
csaw differential binding visualization
csaw
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 140
2
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1
reply
1.4k
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Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ★ 4.8k
3
votes
1
reply
2.2k
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Correct use of TMM / normalization factors based on large bins
csaw TMM
5.7 years ago ATpoint ★ 4.8k
1
vote
7
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2.2k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
6
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2
replies
1.9k
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw software error
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 30
3
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7
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5.0k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
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7
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1.7k
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A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
6.4 years ago sorjuelal • 0
0
votes
4
replies
2.1k
views
csaw spike-in normalization
ChIP-seq csaw
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 260
0
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1
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1.1k
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Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 170
1
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3
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1.7k
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CSAW ready to use R script
csaw
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 10
0
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1
reply
1.6k
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Best csaw normalization approach for ATAC-seq data
csaw
updated 6.6 years ago by ★ 28k • written 6.7 years ago by ▴ 60
0
votes
2
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1.3k
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 6.8 years ago by ★ 28k • written 6.8 years ago by ★ 2.0k
2
votes
5
replies
1.5k
views
Differential ChIP-seq analysis
diffbind csaw
updated 6.8 years ago by ★ 5.2k • written 6.8 years ago by • 0
0
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5
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1.8k
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 6.9 years ago by ★ 28k • written 6.9 years ago by • 0
2
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2
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1.3k
views
csaw: Estimate fragment length
csaw
7.1 years ago nicolas.descostes ▴ 20
0
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3
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1.6k
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csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 7.5 years ago by 25k • written 7.5 years ago by • 0
3
votes
7
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2.6k
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complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ★ 1.5k
1
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2
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1.2k
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the Normalise function in csaw
csaw
7.5 years ago tangj ▴ 10
0
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2
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1.5k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 7.6 years ago by ★ 28k • written 7.6 years ago by • 0
2
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2
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1.4k
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csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 40
3
votes
3
replies
2.0k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 7.6 years ago by ★ 28k • written 7.6 years ago by • 0
3
votes
11
replies
2.9k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 7.7 years ago by ★ 7.9k • written 7.7 years ago by ▴ 10
1
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2
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1.5k
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 100
2
votes
2
replies
1.2k
views
Run windowCounts only on annotated regions?
csaw
updated 8.2 years ago by ★ 28k • written 8.2 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 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 70
3
votes
6
replies
2.3k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
3
votes
3
replies
2.0k
views
Use csaw to build matrix for heatmap?
csaw chipseq edger
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
3
votes
4
replies
2.4k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 8.3 years ago by ★ 28k • written 8.3 years ago by • 0
4
votes
2
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2.8k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 20
2
votes
11
replies
2.3k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
8.6 years ago endrebak85 ▴ 40
2
votes
2
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1.4k
views
csaw: removing PCR duplicates using dedup flag
csaw dedup
updated 8.6 years ago by 68k • written 8.6 years ago by • 0
2
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1
reply
2.2k
views
csaw with negative controls
csaw
8.8 years ago chriad ▴ 10
5
votes
6
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2.4k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
8.9 years ago saadmurtazakhan ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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