Showing : csaw • reset
3
votes
4
replies
324
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
7 weeks ago • updated 4 weeks ago spg • 0
0
votes
0
replies
104
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
7 weeks ago Bogdan ▴ 660
1
vote
2
replies
587
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
9 months ago zgraytho88 • 0
1
vote
2
replies
547
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 10 months ago by ★ 4.6k • written 10 months ago by • 0
0
votes
2
replies
318
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw csawUsersGuide
updated 15 months ago by ★ 28k • written 15 months ago by • 0
0
votes
1
reply
737
views
[CSAW] Erreur : Negative counts not allowed
csaw
16 months ago Nicolas Servant ▴ 260
3
votes
5
replies
1.4k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 2.3 years ago by ▴ 10 • written 2.3 years ago by ▴ 50
2
votes
1
reply
714
views
normOffsets in csaw
csaw
updated 2.4 years ago by ★ 28k • written 2.4 years ago by ★ 2.1k
1
vote
2
replies
678
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 2.4 years ago by ★ 28k • written 2.4 years ago by ▴ 50
0
votes
4
replies
901
views
DiffBind or csaw between different transcription factors
DiffBind csaw
updated 2.6 years ago by ★ 28k • written 2.6 years ago by ▴ 20
1
vote
3
replies
597
views
csaw differential binding visualization
csaw
updated 2.8 years ago by ★ 28k • written 2.8 years ago by ▴ 140
2
votes
1
reply
502
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 3.1 years ago by ★ 28k • written 3.1 years ago by ★ 2.1k
3
votes
1
reply
982
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
3.4 years ago ATpoint ★ 2.1k
1
vote
7
replies
956
views
Error while running normOffsets in diffhic
diffhic csaw
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
6
votes
2
replies
881
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw software error
updated 3.6 years ago by 25k • written 3.6 years ago by ▴ 20
3
votes
7
replies
2.4k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 4.1 years ago by 39k • written 4.1 years ago by • 0
0
votes
7
replies
749
views
A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
4.2 years ago sorjuelal • 0
0
votes
4
replies
835
views
csaw spike-in normalization
ChIP-seq csaw
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 260
0
votes
1
reply
597
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ▴ 90
1
vote
3
replies
939
views
CSAW ready to use R script
csaw
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ▴ 10
0
votes
1
reply
811
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 4.4 years ago by ★ 28k • written 4.5 years ago by ▴ 60
0
votes
2
replies
621
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ★ 2.0k
2
votes
5
replies
827
views
Differential ChIP-seq analysis
diffbind csaw
updated 4.6 years ago by ★ 4.6k • written 4.6 years ago by • 0
0
votes
5
replies
872
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 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
2
votes
2
replies
809
views
csaw: Estimate fragment length
csaw
4.9 years ago nicolas.descostes ▴ 20
0
votes
3
replies
875
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 5.3 years ago by 25k • written 5.3 years ago by • 0
3
votes
7
replies
1.2k
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ★ 1.5k
1
vote
2
replies
686
views
the Normalise function in csaw
csaw
5.3 years ago tangj ▴ 10
0
votes
2
replies
846
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
2
votes
2
replies
780
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 30
3
votes
3
replies
1.0k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
3
votes
11
replies
1.8k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 5.5 years ago by 7.8k • written 5.5 years ago by ▴ 10
1
vote
2
replies
900
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 100
2
votes
2
replies
720
views
Run windowCounts only on annotated regions?
csaw
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 30
3
votes
1
reply
1.2k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw limma sva qsmooth edger
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 70
3
votes
6
replies
1.3k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 6.0 years ago by ★ 28k • written 6.0 years ago by • 0
3
votes
3
replies
1.1k
views
Use csaw to build matrix for heatmap?
csaw chipseq edger
updated 6.0 years ago by ★ 28k • written 6.0 years ago by • 0
3
votes
4
replies
1.4k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 6.1 years ago by ★ 28k • written 6.1 years ago by • 0
3
votes
2
replies
1.6k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 10
2
votes
11
replies
1.4k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
6.3 years ago endrebak85 ▴ 30
2
votes
2
replies
796
views
csaw: removing PCR duplicates using dedup flag
csaw dedup
updated 6.3 years ago by 62k • written 6.3 years ago by • 0
2
votes
1
reply
1.5k
views
csaw with negative controls
csaw
6.6 years ago chriad ▴ 10
5
votes
6
replies
1.4k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
6.7 years ago saadmurtazakhan ▴ 10
1
vote
18
replies
2.4k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 10
1
vote
3
replies
1.6k
views
csaw filterWindows function results in a warning: ("Zero library size detected.")
csaw
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 10
3
votes
1
reply
1.0k
views
window counts in csaw
csaw counts
updated 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
2
votes
1
reply
778
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 6.8 years ago by ★ 28k • written 6.8 years ago by ▴ 30
1
vote
3
replies
880
views
csaw: dumpPE on multiple bam files.
csaw dumpPE windowCounts
7.2 years ago • updated 6.8 years ago asif.zubair • 0
1
vote
1
reply
641
views
csaw: post clustering description of regions
csaw mergeWindows
updated 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
3
votes
2
replies
806
views
csaw: when not to dedup
csaw dedup
updated 17 months ago by • 0 • written 6.8 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: TCGA: clinical data and expression data by sharifnstu1203002m • 0
Hello, I am in the same problem. I downloaded "transcriptome profiling" data of TCGA by using the Bioconductor package. I get my gene expr…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Jonathan Göke ▴ 40
Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R by Gordon Smyth 47k
Choosing which samples to normalize together is not dependent on library size but rather on (1) whether the tissue samples are comparable a…
Comment: Atena package - error (new user) by lalanis1 • 0
Thanks a lot, Calvo. Will run my files with revised version soon! Best regards, Lalani
Comment: Nested paired design with covariates in limma by Gordon Smyth 47k
Please post a new question with enough detail to answer your question. If you want bespoke advance, then you need to post the details of yo…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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