Showing : Csaw • reset
2
votes
7
replies
1.5k
views
CSAW: GAIN and LOSS of enrichment
csaw
updated 8.2 years ago by ▴ 10 • written 9.1 years ago by • 0
1
vote
7
replies
1.2k
views
CSAW: filtering prior information
csaw
8.9 years ago sergio.espeso-gil • 0
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
7
replies
1.3k
views
CSAW: Annotation through clustering with external information
csaw
updated 8.7 years ago by 50k • written 8.7 years ago by • 0
3
votes
2
replies
3.5k
views
TMM normalisation method
Csaw csaw
9.2 years ago • updated 9.1 years ago sergio.espeso-gil • 0
4
votes
2
replies
1.4k
views
Csaw : filter windows based on matched negative control
csaw differential binding analysis
8.6 years ago Pierre-François Roux • 0
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
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
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
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
1
vote
1
reply
1.6k
views
Differential binding using csaw
csaw differential binding analysis chipseq differential expression differential gene expression
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 10
2
votes
3
replies
1.2k
views
Unexpected reversal in normalization factors from csaw
csaw normalization
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ★ 7.9k
2
votes
1
reply
1.3k
views
Strategy for choosing window size and read extension length for csaw?
csaw differential binding analysis bin size
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ★ 7.9k
4
votes
1
reply
2.8k
views
csaw - workflow to incorporate input/control samples?
csaw chipseq differential binding analysis
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 10
3
votes
1
reply
894
views
Detection of methylated regions from MeDIP data using csaw
csaw medip-chip
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
3
votes
2
replies
1.1k
views
csaw: when not to dedup
csaw dedup
updated 2.7 years ago by • 0 • written 8.0 years ago by • 0
1
vote
1
reply
879
views
csaw: post clustering description of regions
csaw mergeWindows
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
2
votes
1
reply
1.0k
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 40
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
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
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
5
votes
6
replies
2.0k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
7.9 years ago saadmurtazakhan ▴ 10
2
votes
1
reply
1.9k
views
csaw with negative controls
csaw
7.8 years ago chriad ▴ 10
2
votes
2
replies
1.1k
views
csaw: removing PCR duplicates using dedup flag
csaw dedup
updated 7.6 years ago by 65k • written 7.6 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
3
votes
4
replies
2.0k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
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
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
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
2
votes
2
replies
940
views
Run windowCounts only on annotated regions?
csaw
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 40
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
3
votes
11
replies
2.3k
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
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
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
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
1
vote
2
replies
996
views
the Normalise function in csaw
csaw
6.6 years ago tangj ▴ 10
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
2
votes
2
replies
1.1k
views
csaw: Estimate fragment length
csaw
6.2 years ago nicolas.descostes ▴ 20
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
0
votes
2
replies
999
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
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
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
866
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
0
votes
4
replies
1.4k
views
csaw spike-in normalization
ChIP-seq csaw
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 260
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
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
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
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
2
votes
1
reply
954
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
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: Create protein sequences including variants from a VCF file by Yun • 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization? by Daniel • 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Guido Hooiveld ★ 4.0k
FWIW: based on [previous posts][1] it is suggested to install like this: install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, typ…
Votes
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
Answer: How to design DEXSeq formula for multiple variables
Awards • All
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to boczniak767 ▴ 720
Popular Question to jmoon1194 • 0
Popular Question to mat.lesche ▴ 90
Popular Question to jordi.planells • 0
Locations • All
France, just now
Sweden, 7 minutes ago
Israel, 10 minutes ago
United States, 11 minutes ago
United States, 14 minutes ago
Traffic: 865 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