Showing : Csaw • reset
0
votes
0
replies
352
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
6 months ago jared.andrews07 ▴ 30
0
votes
0
replies
359
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount csaw paired
10 months ago julie.chevalier • 0
2
votes
4
replies
945
views
Error with regionCounts()
csaw
13 months ago Chris ▴ 10
0
votes
0
replies
427
views
some questions about eliminating efficiency biaes in csaw user's guide
csawUsersGuide csaw
15 months ago sashu • 0
3
votes
4
replies
1.7k
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
0
votes
0
replies
462
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
17 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 2.1 years ago by • 0
1
vote
2
replies
1.3k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.2 years ago by ★ 5.2k • written 2.2 years ago by • 0
0
votes
2
replies
677
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
1.6k
views
[CSAW] Erreur : Negative counts not allowed
csaw
2.6 years ago Nicolas Servant ▴ 260
3
votes
5
replies
2.6k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 3.6 years ago by ▴ 10 • written 3.6 years ago by ▴ 50
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
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
962
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
1.7k
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 4.9 years ago by 25k • written 4.9 years ago by ▴ 30
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
0
votes
7
replies
1.3k
views
A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
5.5 years ago sorjuelal • 0
0
votes
4
replies
1.4k
views
csaw spike-in normalization
ChIP-seq csaw
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 260
0
votes
1
reply
869
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
updated 5.7 years ago by ★ 28k • written 5.7 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
1.0k
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
1.2k
views
Differential ChIP-seq analysis
diffbind csaw
updated 5.9 years ago by ★ 5.2k • written 5.9 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 6.0 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 6.6 years ago by 25k • written 6.6 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 6.6 years ago by ★ 28k • written 6.6 years ago by ★ 1.5k
1
vote
2
replies
999
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 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
2
votes
2
replies
1.1k
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 6.7 years ago by ★ 28k • written 6.7 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
2.4k
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 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 100
2
votes
2
replies
946
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
2.0k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 7.4 years ago by ★ 28k • written 7.4 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 66k • written 7.6 years ago by • 0
2
votes
1
reply
1.9k
views
csaw with negative controls
csaw
7.9 years ago chriad ▴ 10
5
votes
6
replies
2.0k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
8.0 years ago saadmurtazakhan ▴ 10
1
vote
18
replies
3.3k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 8.0 years ago by ★ 28k • written 8.0 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
Recent ...
Replies
Comment: slingshot: error with plot3d.SlingshotDataSet by Happiness • 0
Hi please i am encountering similar issue how did you fix it. Here is the code: ## Run Slingshot p3.neuron.sds <- slingshot(Embeddings(…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by mohammedtoufiq91 ▴ 10
https://support.bioconductor.org/u/5106/ thank you very much.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Thank you so much!
Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Votes
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Awards • All
Scholar to Mike Smith ★ 6.5k
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to bas_work ▴ 30
Popular Question to landenshanie ▴ 40
Locations • All
Vietnam, 23 minutes ago
Hong Kong, 45 minutes ago
WEHI, Melbourne, Australia, 52 minutes ago
United States, 59 minutes ago
China, 1 hour ago
Traffic: 517 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6