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Showing :
csaw
•
reset
3
votes
4
replies
324
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
7 weeks ago • updated 4 weeks ago
spg
• 0
0
votes
0
replies
104
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma
edgeR
csaw
7 weeks ago
Bogdan
▴ 660
1
vote
2
replies
587
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq
regionCounts
csaw
9 months ago
zgraytho88
• 0
1
vote
2
replies
547
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 10 months ago by
Rory Stark
★ 4.6k • written 10 months ago by
maria.soler
• 0
0
votes
2
replies
318
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw
csawUsersGuide
updated 15 months ago by
Aaron Lun
★ 28k • written 15 months ago by
kimmai.phan
• 0
0
votes
1
reply
737
views
[CSAW] Erreur : Negative counts not allowed
csaw
16 months ago
Nicolas Servant
▴ 260
3
votes
5
replies
1.4k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw
ATAC-seq
Tn5 insertions
updated 2.3 years ago by
Antonio Ahn
▴ 10 • written 2.3 years ago by
alexandre.blais
▴ 50
2
votes
1
reply
714
views
normOffsets in csaw
csaw
updated 2.4 years ago by
Aaron Lun
★ 28k • written 2.4 years ago by
ATpoint
★ 2.1k
1
vote
2
replies
678
views
Error in csaw::windowCounts when using readParam
csaw
GenomeInfoDb
updated 2.4 years ago by
Aaron Lun
★ 28k • written 2.4 years ago by
RichardJActon
▴ 50
0
votes
4
replies
901
views
DiffBind or csaw between different transcription factors
DiffBind
csaw
updated 2.6 years ago by
Aaron Lun
★ 28k • written 2.6 years ago by
GFM
▴ 20
1
vote
3
replies
597
views
csaw differential binding visualization
csaw
updated 2.8 years ago by
Aaron Lun
★ 28k • written 2.8 years ago by
C T
▴ 140
2
votes
1
reply
502
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw
chip-seq
updated 3.1 years ago by
Aaron Lun
★ 28k • written 3.1 years ago by
ATpoint
★ 2.1k
3
votes
1
reply
982
views
Correct use of TMM / normalization factors based on large bins
csaw
TMM
3.4 years ago
ATpoint
★ 2.1k
1
vote
7
replies
956
views
Error while running normOffsets in diffhic
diffhic
csaw
updated 3.5 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
shopnil99
• 0
6
votes
2
replies
881
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw
software error
updated 3.6 years ago by
Martin Morgan
25k • written 3.6 years ago by
vanbelj
▴ 20
3
votes
7
replies
2.4k
views
DEseq2 for differential binding analysis ChIP seq
deseq2
diffbind
csaw
greylistchip
chipseq
updated 4.1 years ago by
Michael Love
39k • written 4.1 years ago by
Yonatan Amzaleg
• 0
0
votes
7
replies
749
views
A problem with csaw that I don't think is a problem with csaw
csaw
caught segfault
4.2 years ago
sorjuelal
• 0
0
votes
4
replies
835
views
csaw spike-in normalization
ChIP-seq
csaw
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
Nicolas Servant
▴ 260
0
votes
1
reply
597
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma
csaw
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
gabriel.hoffman
▴ 90
1
vote
3
replies
939
views
CSAW ready to use R script
csaw
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
polaxgr
▴ 10
0
votes
1
reply
811
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
Lucy
▴ 60
0
votes
2
replies
621
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
Jenny Drnevich
★ 2.0k
2
votes
5
replies
827
views
Differential ChIP-seq analysis
diffbind
csaw
updated 4.6 years ago by
Rory Stark
★ 4.6k • written 4.6 years ago by
bioinfo
• 0
0
votes
5
replies
872
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 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
94133
• 0
2
votes
2
replies
809
views
csaw: Estimate fragment length
csaw
4.9 years ago
nicolas.descostes
▴ 20
0
votes
3
replies
875
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic
csaw
Rhtslib
updated 5.3 years ago by
Martin Morgan
25k • written 5.3 years ago by
favorov
• 0
3
votes
7
replies
1.2k
views
complex design for chip-seq analysis
chipseq
csaw
limma
design matrix
multiple factor design
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
Assa Yeroslaviz
★ 1.5k
1
vote
2
replies
686
views
the Normalise function in csaw
csaw
5.3 years ago
tangj
▴ 10
0
votes
2
replies
846
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw
histone chip-seq
chip-seq
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
gil.hornung
• 0
2
votes
2
replies
780
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
endrebak85
▴ 30
3
votes
3
replies
1.0k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw
differential binding analysis
sample size
independent filtering
statistical power
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
zhangly811
• 0
3
votes
11
replies
1.8k
views
Exporting normalized counts over final DB windows from csaw
csaw
edger
chip-seq
updated 5.5 years ago by
Ryan C. Thompson
7.8k • written 5.5 years ago by
jms1223
▴ 10
1
vote
2
replies
900
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
Vivek.b
▴ 100
2
votes
2
replies
720
views
Run windowCounts only on annotated regions?
csaw
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
endrebak85
▴ 30
3
votes
1
reply
1.2k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw
limma
sva
qsmooth
edger
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
jma1991
▴ 70
3
votes
6
replies
1.3k
views
Differential Pol2 pausing analysis
edger
csaw
chipseq
differential binding analysis
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
dalerr
• 0
3
votes
3
replies
1.1k
views
Use csaw to build matrix for heatmap?
csaw
chipseq
edger
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
jmKeith
• 0
3
votes
4
replies
1.4k
views
Interpretation of cross correlation plot to determine fragment length
csaw
chip-seq
histone
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
siklenkak
• 0
3
votes
2
replies
1.6k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw
chip-seq
normalization
edger
cqn
updated 6.3 years ago by
Aaron Lun
★ 28k • written 6.3 years ago by
s1437643
▴ 10
2
votes
11
replies
1.4k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
6.3 years ago
endrebak85
▴ 30
2
votes
2
replies
796
views
csaw: removing PCR duplicates using dedup flag
csaw
dedup
updated 6.3 years ago by
James W. MacDonald
62k • written 6.3 years ago by
asif.zubair
• 0
2
votes
1
reply
1.5k
views
csaw with negative controls
csaw
6.6 years ago
chriad
▴ 10
5
votes
6
replies
1.4k
views
Getting normalized read counts from region counts
regionCounts
TMM
csaw
6.7 years ago
saadmurtazakhan
▴ 10
1
vote
18
replies
2.4k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq
TSS
TMM
csaw
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
saadmurtazakhan
▴ 10
1
vote
3
replies
1.6k
views
csaw filterWindows function results in a warning: ("Zero library size detected.")
csaw
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
chriad
▴ 10
3
votes
1
reply
1.0k
views
window counts in csaw
csaw
counts
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
nobishvarghese
• 0
2
votes
1
reply
778
views
How does csaw handle multiply aligned reads?
csaw
chip-seq
updated 6.8 years ago by
Aaron Lun
★ 28k • written 6.8 years ago by
endrebak85
▴ 30
1
vote
3
replies
880
views
csaw: dumpPE on multiple bam files.
csaw
dumpPE
windowCounts
7.2 years ago • updated 6.8 years ago
asif.zubair
• 0
1
vote
1
reply
641
views
csaw: post clustering description of regions
csaw
mergeWindows
updated 6.8 years ago by
Aaron Lun
★ 28k • written 6.8 years ago by
asif.zubair
• 0
3
votes
2
replies
806
views
csaw: when not to dedup
csaw
dedup
updated 17 months ago by
uli.arb
• 0 • written 6.8 years ago by
asif.zubair
• 0
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