Showing : csaw • reset
1
vote
3
replies
336
views
Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 18 hours ago by • 0 • written 4 days ago by • 0
0
votes
0
replies
679
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
14 months ago jared.andrews07 ▴ 30
0
votes
0
replies
536
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount csaw paired
19 months ago julie.chevalier • 0
2
votes
4
replies
1.3k
views
Error with regionCounts()
csaw
22 months ago Chris ▴ 20
0
votes
0
replies
607
views
some questions about eliminating efficiency biaes in csaw user's guide
csawUsersGuide csaw
23 months ago sashu • 0
3
votes
4
replies
2.4k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
2.1 years ago spg • 0
0
votes
0
replies
632
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
2.1 years ago Bogdan ▴ 670
1
vote
3
replies
2.0k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 14 months ago by • 0 • written 2.7 years ago by • 0
1
vote
2
replies
1.7k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.9 years ago by ★ 5.2k • written 2.9 years ago by • 0
0
votes
2
replies
856
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw csawUsersGuide
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
0
votes
1
reply
1.9k
views
[CSAW] Erreur : Negative counts not allowed
csaw
3.3 years ago Nicolas Servant ▴ 260
3
votes
5
replies
3.2k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 4.3 years ago by ▴ 10 • written 4.3 years ago by ▴ 50
2
votes
1
reply
1.5k
views
normOffsets in csaw
csaw
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ★ 4.6k
1
vote
2
replies
1.4k
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ▴ 50
0
votes
4
replies
2.1k
views
DiffBind or csaw between different transcription factors
DiffBind csaw
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 20
1
vote
3
replies
1.4k
views
csaw differential binding visualization
csaw
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 140
2
votes
1
reply
1.2k
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ★ 4.6k
3
votes
1
reply
2.0k
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
5.4 years ago ATpoint ★ 4.6k
1
vote
7
replies
2.1k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
6
votes
2
replies
1.8k
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw software error
updated 5.6 years ago by 25k • written 5.6 years ago by ▴ 30
3
votes
7
replies
4.6k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
0
votes
7
replies
1.6k
views
A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
6.2 years ago sorjuelal • 0
0
votes
4
replies
1.9k
views
csaw spike-in normalization
ChIP-seq csaw
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 260
0
votes
1
reply
1.0k
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 170
1
vote
3
replies
1.6k
views
CSAW ready to use R script
csaw
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 60
0
votes
2
replies
1.2k
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ★ 2.0k
2
votes
5
replies
1.4k
views
Differential ChIP-seq analysis
diffbind csaw
updated 6.6 years ago by ★ 5.2k • written 6.6 years ago by • 0
0
votes
5
replies
1.6k
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 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
2
votes
2
replies
1.3k
views
csaw: Estimate fragment length
csaw
6.9 years ago nicolas.descostes ▴ 20
0
votes
3
replies
1.5k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 7.3 years ago by 25k • written 7.3 years ago by • 0
3
votes
7
replies
2.4k
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ★ 1.5k
1
vote
2
replies
1.2k
views
the Normalise function in csaw
csaw
7.3 years ago tangj ▴ 10
0
votes
2
replies
1.4k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
2
votes
2
replies
1.3k
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 40
3
votes
3
replies
1.9k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
3
votes
11
replies
2.7k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 7.5 years ago by ★ 7.9k • written 7.5 years ago by ▴ 10
1
vote
2
replies
1.4k
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 100
2
votes
2
replies
1.1k
views
Run windowCounts only on annotated regions?
csaw
updated 7.9 years ago by ★ 28k • written 7.9 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 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 70
3
votes
6
replies
2.2k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
3
votes
3
replies
1.8k
views
Use csaw to build matrix for heatmap?
csaw chipseq edger
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
3
votes
4
replies
2.3k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 8.1 years ago by ★ 28k • written 8.1 years ago by • 0
4
votes
2
replies
2.6k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 20
2
votes
11
replies
2.1k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
8.3 years ago endrebak85 ▴ 40
2
votes
2
replies
1.3k
views
csaw: removing PCR duplicates using dedup flag
csaw dedup
updated 8.3 years ago by 67k • written 8.3 years ago by • 0
2
votes
1
reply
2.1k
views
csaw with negative controls
csaw
8.6 years ago chriad ▴ 10
5
votes
6
replies
2.3k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
8.6 years ago saadmurtazakhan ▴ 10
1
vote
18
replies
3.8k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 10
1
vote
3
replies
2.1k
views
csaw filterWindows function results in a warning: ("Zero library size detected.")
csaw
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
Votes
A: PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
Awards • All
Popular Question to Maria Doyle ▴ 100
Popular Question to Robert Ivanek ▴ 750
Popular Question to shepherl 4.1k
Popular Question to Gordon Smyth 52k
Popular Question to Koen Van den Berge ▴ 180
Locations • All
United States, 17 minutes ago
The city by the bay, 47 minutes ago
United States, 1 hour ago
United States, 1 hour ago
WEHI, Melbourne, Australia, 2 hours ago
Traffic: 516 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