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Showing :
csaw
•
reset
1
vote
8
replies
2.7k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
8 months ago • updated 7 months ago
Luca
• 0
0
votes
1
reply
406
views
Restricting differential binding analysis to only TSS-proximal regions
ChIP
csaw
updated 10 months ago by
Aaron Lun
★ 29k • written 10 months ago by
Luca
• 0
1
vote
3
replies
1.2k
views
Csaw normalization strategies - general inquiry
ChIPSeq
csaw
updated 10 months ago by
franknappi14
• 0 • written 10 months ago by
Luca
• 0
0
votes
0
replies
1.0k
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
2.1 years ago
jared.andrews07
▴ 30
0
votes
0
replies
710
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount
csaw
paired
2.4 years ago
julie.chevalier
• 0
2
votes
4
replies
1.7k
views
Error with regionCounts()
csaw
2.7 years ago
Chris
▴ 20
0
votes
0
replies
786
views
some questions about eliminating efficiency biaes in csaw user's guide
csawUsersGuide
csaw
2.8 years ago
sashu
• 0
3
votes
4
replies
3.1k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
3.0 years ago • updated 2.9 years ago
spg
• 0
0
votes
0
replies
805
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma
edgeR
csaw
3.0 years ago
Bogdan
▴ 670
1
vote
3
replies
2.5k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq
regionCounts
csaw
updated 2.0 years ago by
dineika.chandrananda
• 0 • written 3.6 years ago by
zgraytho88
• 0
1
vote
2
replies
2.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 3.7 years ago by
Rory Stark
★ 5.2k • written 3.7 years ago by
maria.soler
• 0
0
votes
2
replies
1.1k
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw
csawUsersGuide
updated 4.1 years ago by
Aaron Lun
★ 29k • written 4.1 years ago by
kimmai.phan
• 0
0
votes
1
reply
2.1k
views
[CSAW] Erreur : Negative counts not allowed
csaw
4.2 years ago
Nicolas Servant
▴ 260
3
votes
5
replies
3.8k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw
ATAC-seq
Tn5 insertions
updated 5.1 years ago by
Antonio Ahn
▴ 10 • written 5.1 years ago by
alexandre.blais
▴ 50
2
votes
1
reply
1.7k
views
normOffsets in csaw
csaw
updated 5.2 years ago by
Aaron Lun
★ 29k • written 5.2 years ago by
ATpoint
★ 5.0k
1
vote
2
replies
1.7k
views
Error in csaw::windowCounts when using readParam
csaw
GenomeInfoDb
updated 5.3 years ago by
Aaron Lun
★ 29k • written 5.3 years ago by
RichardJActon
▴ 50
0
votes
4
replies
2.5k
views
DiffBind or csaw between different transcription factors
DiffBind
csaw
updated 5.5 years ago by
Aaron Lun
★ 29k • written 5.5 years ago by
GFM
▴ 20
1
vote
3
replies
1.8k
views
csaw differential binding visualization
csaw
updated 5.7 years ago by
Aaron Lun
★ 29k • written 5.7 years ago by
C T
▴ 140
2
votes
1
reply
1.6k
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw
chip-seq
updated 6.0 years ago by
Aaron Lun
★ 29k • written 6.0 years ago by
ATpoint
★ 5.0k
3
votes
1
reply
2.4k
views
Correct use of TMM / normalization factors based on large bins
csaw
TMM
6.3 years ago
ATpoint
★ 5.0k
1
vote
7
replies
2.5k
views
Error while running normOffsets in diffhic
diffhic
csaw
updated 6.3 years ago by
Aaron Lun
★ 29k • written 6.3 years ago by
shopnil99
• 0
6
votes
2
replies
2.1k
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw
software error
updated 6.4 years ago by
Martin Morgan
25k • written 6.4 years ago by
vanbelj
▴ 30
3
votes
7
replies
5.5k
views
DEseq2 for differential binding analysis ChIP seq
deseq2
diffbind
csaw
greylistchip
chipseq
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
Yonatan Amzaleg
• 0
0
votes
7
replies
2.0k
views
A problem with csaw that I don't think is a problem with csaw
csaw
caught segfault
7.0 years ago
sorjuelal
• 0
0
votes
4
replies
2.4k
views
csaw spike-in normalization
ChIP-seq
csaw
updated 7.1 years ago by
Aaron Lun
★ 29k • written 7.1 years ago by
Nicolas Servant
▴ 260
0
votes
1
reply
1.2k
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma
csaw
updated 7.2 years ago by
Aaron Lun
★ 29k • written 7.2 years ago by
gabriel.hoffman
▴ 170
1
vote
3
replies
1.8k
views
CSAW ready to use R script
csaw
updated 7.2 years ago by
Aaron Lun
★ 29k • written 7.2 years ago by
polaxgr
▴ 10
0
votes
1
reply
1.8k
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 7.2 years ago by
Aaron Lun
★ 29k • written 7.3 years ago by
Lucy
▴ 60
0
votes
2
replies
1.5k
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 7.4 years ago by
Aaron Lun
★ 29k • written 7.4 years ago by
Jenny Drnevich
★ 2.0k
2
votes
5
replies
1.8k
views
Differential ChIP-seq analysis
diffbind
csaw
updated 7.4 years ago by
Rory Stark
★ 5.2k • written 7.4 years ago by
bioinfo
• 0
0
votes
5
replies
2.0k
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 7.5 years ago by
Aaron Lun
★ 29k • written 7.5 years ago by
94133
• 0
2
votes
2
replies
1.5k
views
csaw: Estimate fragment length
csaw
7.7 years ago
nicolas.descostes
▴ 20
0
votes
3
replies
1.8k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic
csaw
Rhtslib
updated 8.1 years ago by
Martin Morgan
25k • written 8.1 years ago by
favorov
• 0
3
votes
7
replies
3.0k
views
complex design for chip-seq analysis
chipseq
csaw
limma
design matrix
multiple factor design
updated 8.1 years ago by
Aaron Lun
★ 29k • written 8.1 years ago by
Assa Yeroslaviz
★ 1.5k
1
vote
2
replies
1.4k
views
the Normalise function in csaw
csaw
8.2 years ago
tangj
▴ 10
0
votes
2
replies
1.8k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw
histone chip-seq
chip-seq
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
gil.hornung
• 0
2
votes
2
replies
1.5k
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
endrebak85
▴ 40
3
votes
3
replies
2.2k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw
differential binding analysis
sample size
independent filtering
statistical power
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
zhangly811
• 0
3
votes
11
replies
3.2k
views
Exporting normalized counts over final DB windows from csaw
csaw
edger
chip-seq
updated 8.4 years ago by
Ryan C. Thompson
★ 7.9k • written 8.4 years ago by
jms1223
▴ 10
1
vote
2
replies
1.7k
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 8.7 years ago by
Aaron Lun
★ 29k • written 8.7 years ago by
Vivek.b
▴ 100
2
votes
2
replies
1.3k
views
Run windowCounts only on annotated regions?
csaw
updated 8.8 years ago by
Aaron Lun
★ 29k • written 8.8 years ago by
endrebak85
▴ 40
3
votes
1
reply
2.0k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw
limma
sva
qsmooth
edger
updated 8.8 years ago by
Aaron Lun
★ 29k • written 8.8 years ago by
jma1991
▴ 70
3
votes
6
replies
2.5k
views
Differential Pol2 pausing analysis
edger
csaw
chipseq
differential binding analysis
updated 8.8 years ago by
Aaron Lun
★ 29k • written 8.8 years ago by
dalerr
• 0
3
votes
3
replies
2.1k
views
Use csaw to build matrix for heatmap?
csaw
chipseq
edger
updated 8.8 years ago by
Aaron Lun
★ 29k • written 8.8 years ago by
jmKeith
• 0
3
votes
4
replies
2.7k
views
Interpretation of cross correlation plot to determine fragment length
csaw
chip-seq
histone
updated 8.9 years ago by
Aaron Lun
★ 29k • written 8.9 years ago by
siklenkak
• 0
4
votes
2
replies
3.0k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw
chip-seq
normalization
edger
cqn
updated 9.1 years ago by
Aaron Lun
★ 29k • written 9.1 years ago by
s1437643
▴ 20
2
votes
11
replies
2.5k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
9.2 years ago
endrebak85
▴ 40
2
votes
2
replies
1.6k
views
csaw: removing PCR duplicates using dedup flag
csaw
dedup
updated 9.2 years ago by
James W. MacDonald
68k • written 9.2 years ago by
asif.zubair
• 0
2
votes
1
reply
2.3k
views
csaw with negative controls
csaw
9.4 years ago
chriad
▴ 10
5
votes
6
replies
2.7k
views
Getting normalized read counts from region counts
regionCounts
TMM
csaw
9.5 years ago
saadmurtazakhan
▴ 10
75 results • Page
1 of 2
Recent ...
Replies
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR
by
efoss
▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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