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Csaw
•
reset
0
votes
0
replies
329
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
5 months ago
jared.andrews07
▴ 30
0
votes
0
replies
341
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount
csaw
paired
10 months ago
julie.chevalier
• 0
2
votes
4
replies
921
views
Error with regionCounts()
csaw
13 months ago
Chris
• 0
0
votes
0
replies
410
views
some questions about eliminating efficiency biaes in csaw user's guide
csawUsersGuide
csaw
14 months ago
sashu
• 0
3
votes
4
replies
1.6k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
16 months ago
spg
• 0
0
votes
0
replies
448
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma
edgeR
csaw
16 months ago
Bogdan
▴ 670
1
vote
3
replies
1.6k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq
regionCounts
csaw
updated 4 months ago by
dineika.chandrananda
• 0 • written 24 months ago by
zgraytho88
• 0
1
vote
2
replies
1.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 2.1 years ago by
Rory Stark
★ 5.2k • written 2.1 years ago by
maria.soler
• 0
0
votes
2
replies
664
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw
csawUsersGuide
updated 2.5 years ago by
Aaron Lun
★ 28k • written 2.5 years ago by
kimmai.phan
• 0
0
votes
1
reply
1.5k
views
[CSAW] Erreur : Negative counts not allowed
csaw
2.6 years ago
Nicolas Servant
▴ 260
3
votes
5
replies
2.5k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw
ATAC-seq
Tn5 insertions
updated 3.5 years ago by
Antonio Ahn
▴ 10 • written 3.5 years ago by
alexandre.blais
▴ 50
2
votes
1
reply
1.2k
views
normOffsets in csaw
csaw
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
ATpoint
★ 4.1k
1
vote
2
replies
1.2k
views
Error in csaw::windowCounts when using readParam
csaw
GenomeInfoDb
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
RichardJActon
▴ 50
0
votes
4
replies
1.6k
views
DiffBind or csaw between different transcription factors
DiffBind
csaw
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
GFM
▴ 20
1
vote
3
replies
1.1k
views
csaw differential binding visualization
csaw
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
C T
▴ 140
2
votes
1
reply
941
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw
chip-seq
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
ATpoint
★ 4.1k
3
votes
1
reply
1.6k
views
Correct use of TMM / normalization factors based on large bins
csaw
TMM
4.7 years ago
ATpoint
★ 4.1k
1
vote
7
replies
1.7k
views
Error while running normOffsets in diffhic
diffhic
csaw
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
shopnil99
• 0
6
votes
2
replies
1.5k
views
csaw: Error in path.expand(bam.file) : invalid 'path' argument
csaw
software error
updated 4.8 years ago by
Martin Morgan
25k • written 4.8 years ago by
vanbelj
▴ 30
3
votes
7
replies
3.7k
views
DEseq2 for differential binding analysis ChIP seq
deseq2
diffbind
csaw
greylistchip
chipseq
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
Yonatan Amzaleg
• 0
0
votes
7
replies
1.3k
views
A problem with csaw that I don't think is a problem with csaw
csaw
caught segfault
5.4 years ago
sorjuelal
• 0
0
votes
4
replies
1.4k
views
csaw spike-in normalization
ChIP-seq
csaw
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
Nicolas Servant
▴ 260
0
votes
1
reply
861
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma
csaw
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
gabriel.hoffman
▴ 110
1
vote
3
replies
1.3k
views
CSAW ready to use R script
csaw
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
polaxgr
▴ 10
0
votes
1
reply
1.3k
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Lucy
▴ 60
0
votes
2
replies
989
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
Jenny Drnevich
★ 2.0k
2
votes
5
replies
1.1k
views
Differential ChIP-seq analysis
diffbind
csaw
updated 5.8 years ago by
Rory Stark
★ 5.2k • written 5.8 years ago by
bioinfo
• 0
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 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
94133
• 0
2
votes
2
replies
1.1k
views
csaw: Estimate fragment length
csaw
6.2 years ago
nicolas.descostes
▴ 20
0
votes
3
replies
1.3k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic
csaw
Rhtslib
updated 6.5 years ago by
Martin Morgan
25k • written 6.5 years ago by
favorov
• 0
3
votes
7
replies
2.0k
views
complex design for chip-seq analysis
chipseq
csaw
limma
design matrix
multiple factor design
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
Assa Yeroslaviz
★ 1.5k
1
vote
2
replies
991
views
the Normalise function in csaw
csaw
6.6 years ago
tangj
▴ 10
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 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
gil.hornung
• 0
2
votes
2
replies
1.1k
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
endrebak85
▴ 40
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 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
zhangly811
• 0
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
Ryan C. Thompson
★ 7.9k • written 6.8 years ago by
jms1223
▴ 10
1
vote
2
replies
1.2k
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
Vivek.b
▴ 100
2
votes
2
replies
932
views
Run windowCounts only on annotated regions?
csaw
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
endrebak85
▴ 40
3
votes
1
reply
1.6k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw
limma
sva
qsmooth
edger
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
jma1991
▴ 70
3
votes
6
replies
1.9k
views
Differential Pol2 pausing analysis
edger
csaw
chipseq
differential binding analysis
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
dalerr
• 0
3
votes
3
replies
1.5k
views
Use csaw to build matrix for heatmap?
csaw
chipseq
edger
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
jmKeith
• 0
3
votes
4
replies
1.9k
views
Interpretation of cross correlation plot to determine fragment length
csaw
chip-seq
histone
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
siklenkak
• 0
4
votes
2
replies
2.2k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw
chip-seq
normalization
edger
cqn
updated 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 years ago by
s1437643
▴ 20
2
votes
11
replies
1.8k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
7.6 years ago
endrebak85
▴ 40
2
votes
2
replies
1.1k
views
csaw: removing PCR duplicates using dedup flag
csaw
dedup
updated 7.6 years ago by
James W. MacDonald
65k • written 7.6 years ago by
asif.zubair
• 0
2
votes
1
reply
1.9k
views
csaw with negative controls
csaw
7.8 years ago
chriad
▴ 10
5
votes
6
replies
2.0k
views
Getting normalized read counts from region counts
regionCounts
TMM
csaw
7.9 years ago
saadmurtazakhan
▴ 10
1
vote
18
replies
3.2k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq
TSS
TMM
csaw
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
saadmurtazakhan
▴ 10
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
Aaron Lun
★ 28k • written 8.0 years ago by
chriad
▴ 10
3
votes
1
reply
1.4k
views
window counts in csaw
csaw
counts
updated 8.0 years ago by
Aaron Lun
★ 28k • written 8.0 years ago by
nobishvarghese
• 0
50 results • Page
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Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient
by
JKim
• 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
Comment: Store output of matchPWM()
by
mat149
▴ 70
out <- do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) Error in do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) : '…
Answer: Store output of matchPWM()
by
James W. MacDonald
65k
Something like this? ``` ind <- as.logical(sapply(hitlist, length)) out <- do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) …
Answer: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
This has been asked before, but with a multi factor design, the LFC for coefficient X adjust for the others, in a way that is often hard to…
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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