Showing : csaw • reset
0
votes
2
replies
117
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw csawUsersGuide
updated 10 weeks ago by ★ 27k • written 10 weeks ago by • 0
0
votes
1
reply
196
views
[CSAW] Erreur : Negative counts not allowed
csaw
3 months ago Nicolas Servant ▴ 260
3
votes
5
replies
718
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 15 months ago by ▴ 10 • written 15 months ago by ▴ 40
2
votes
1
reply
412
views
normOffsets in csaw
csaw
updated 16 months ago by ★ 27k • written 16 months ago by ▴ 970
0
votes
2
replies
401
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 17 months ago by ★ 27k • written 17 months ago by ▴ 40
0
votes
4
replies
535
views
DiffBind or csaw between different transcription factors
DiffBind csaw
updated 19 months ago by ★ 27k • written 19 months ago by ▴ 20
1
vote
3
replies
303
views
csaw differential binding visualization
csaw
updated 22 months ago by ★ 27k • written 22 months ago by ▴ 140
2
votes
1
reply
283
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 2.1 years ago by ★ 27k • written 2.1 years ago by ▴ 970
3
votes
1
reply
626
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
2.4 years ago ATpoint ▴ 970
1
vote
7
replies
607
views
Error while running normOffsets in diffhic
diffhic csaw
updated 2.5 years ago by ★ 27k • written 2.5 years ago by • 0
6
votes
2
replies
577
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw software error
updated 2.6 years ago by 25k • written 2.6 years ago by ▴ 10
3
votes
7
replies
1.7k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 3.1 years ago by 35k • written 3.1 years ago by • 0
0
votes
7
replies
565
views
A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
3.2 years ago sorjuelal • 0
0
votes
4
replies
619
views
csaw spike-in normalization
ChIP-seq csaw
updated 3.2 years ago by ★ 27k • written 3.2 years ago by ▴ 260
0
votes
1
reply
478
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw
updated 3.4 years ago by ★ 27k • written 3.4 years ago by ▴ 90
1
vote
3
replies
681
views
CSAW ready to use R script
csaw
updated 3.4 years ago by ★ 27k • written 3.4 years ago by ▴ 10
0
votes
1
reply
583
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 3.4 years ago by ★ 27k • written 3.4 years ago by ▴ 30
0
votes
2
replies
458
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 3.5 years ago by ★ 27k • written 3.5 years ago by ★ 2.0k
2
votes
5
replies
640
views
Differential ChIP-seq analysis
diffbind csaw
updated 3.6 years ago by ★ 4.3k • written 3.6 years ago by • 0
0
votes
5
replies
700
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 3.7 years ago by ★ 27k • written 3.7 years ago by • 0
2
votes
2
replies
635
views
csaw: Estimate fragment length
csaw
3.9 years ago nicolas.descostes ▴ 20
0
votes
3
replies
702
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 4.2 years ago by 25k • written 4.2 years ago by • 0
3
votes
7
replies
872
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 4.3 years ago by ★ 27k • written 4.3 years ago by ★ 1.5k
1
vote
2
replies
531
views
the Normalise function in csaw
csaw
4.3 years ago tangj ▴ 10
0
votes
2
replies
678
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 4.3 years ago by ★ 27k • written 4.3 years ago by • 0
2
votes
2
replies
648
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 4.4 years ago by ★ 27k • written 4.4 years ago by ▴ 30
3
votes
3
replies
808
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 4.4 years ago by ★ 27k • written 4.4 years ago by • 0
2
votes
11
replies
1.5k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 4.5 years ago by 7.7k • written 4.5 years ago by • 0
1
vote
2
replies
774
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 4.8 years ago by ★ 27k • written 4.8 years ago by ▴ 100
2
votes
2
replies
580
views
Run windowCounts only on annotated regions?
csaw
updated 4.9 years ago by ★ 27k • written 4.9 years ago by ▴ 30
3
votes
1
reply
1.1k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw limma sva qsmooth edger
updated 5.0 years ago by ★ 27k • written 5.0 years ago by ▴ 60
3
votes
6
replies
1.1k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 5.0 years ago by ★ 27k • written 5.0 years ago by • 0
3
votes
3
replies
889
views
Use csaw to build matrix for heatmap?
csaw chipseq edger
updated 5.0 years ago by ★ 27k • written 5.0 years ago by • 0
3
votes
4
replies
1.1k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 5.0 years ago by ★ 27k • written 5.0 years ago by • 0
3
votes
2
replies
1.4k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 5.3 years ago by ★ 27k • written 5.3 years ago by ▴ 10
2
votes
11
replies
1.1k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
5.3 years ago endrebak85 ▴ 30
2
votes
2
replies
683
views
csaw: removing PCR duplicates using dedup flag
csaw dedup
updated 5.3 years ago by 58k • written 5.3 years ago by • 0
2
votes
1
reply
1.2k
views
csaw with negative controls
csaw
5.5 years ago chriad ▴ 10
5
votes
6
replies
1.2k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
5.6 years ago saadmurtazakhan ▴ 10
1
vote
18
replies
2.1k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 5.7 years ago by ★ 27k • written 5.7 years ago by ▴ 10
1
vote
3
replies
1.3k
views
csaw filterWindows function results in a warning: ("Zero library size detected.")
csaw
updated 5.7 years ago by ★ 27k • written 5.7 years ago by ▴ 10
3
votes
1
reply
801
views
window counts in csaw
csaw counts
updated 5.7 years ago by ★ 27k • written 5.7 years ago by • 0
2
votes
1
reply
674
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 5.7 years ago by ★ 27k • written 5.7 years ago by ▴ 30
1
vote
3
replies
773
views
csaw: dumpPE on multiple bam files.
csaw dumpPE windowCounts
6.2 years ago • updated 5.7 years ago asif.zubair • 0
1
vote
1
reply
533
views
csaw: post clustering description of regions
csaw mergeWindows
updated 5.7 years ago by ★ 27k • written 5.7 years ago by • 0
3
votes
2
replies
661
views
csaw: when not to dedup
csaw dedup
updated 5 months ago by • 0 • written 5.7 years ago by • 0
3
votes
1
reply
599
views
Detection of methylated regions from MeDIP data using csaw
csaw medip-chip
updated 5.7 years ago by ★ 27k • written 5.7 years ago by • 0
4
votes
1
reply
1.9k
views
csaw - workflow to incorporate input/control samples?
csaw chipseq differential binding analysis
updated 5.7 years ago by ★ 27k • written 5.7 years ago by ▴ 10
2
votes
1
reply
792
views
Strategy for choosing window size and read extension length for csaw?
csaw differential binding analysis bin size
updated 5.8 years ago by ★ 27k • written 5.8 years ago by 7.7k
2
votes
3
replies
791
views
Unexpected reversal in normalization factors from csaw
csaw normalization
updated 5.8 years ago by ★ 27k • written 5.8 years ago by 7.7k
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to use subjunc for differential splicing analysis? by Assa Yeroslaviz ★ 1.5k
I assume, that it would make more sense to quantify the reads based on the gene-level and not the exon-level, following by using the `diffS…
Comment: Reading large file (15GB) in R by nabiyogesh • 0
Thanks Sean, I am getting below error with fread, I am running this on HPC with 500GB. > library(data.table) data.table 1.14.2 u…
Comment: Weird output of DESeq2 when using single sample from one group agains the other by Michael Love 35k
This is why you lose power, yes. Power related to sample size. You are also losing information about within-group variance from one group.…
Comment: Weird output of DESeq2 when using single sample from one group agains the other by FantasticAI • 0
Hi Michael, Thank you for your reply. When you say the degrees of freedom reduces from 10 to 5, is this part of the reason that cause the …
Comment: MotifDb missing some FlyFactor Motifs by gunjan.dikshit • 0
Sure, I could give it a try. Can you guide me regarding it.
Votes
Answer: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
Answer: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
Answer: Joint disperstion estimation for DEXSeq and DESeq2
Answer: Problems to find the pvalues via rowttests
A: How to use subSeq with DNAStringSet and information of GroupedIRanges?
Awards • All
Scholar to Michael Love 35k
Popular Question to Gordon Smyth 44k
Popular Question to floriandeckert ▴ 30
Popular Question to mikhael.manurung ▴ 230
Popular Question to Stephanie M. Gogarten ▴ 820
Locations • All
United States, 18 minutes ago
European Union, 27 minutes ago
Switzerland, 33 minutes ago
United States, 36 minutes ago
CRUK, Cambridge, UK, 43 minutes ago
Traffic: 465 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