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Csaw
•
reset
0
votes
0
replies
413
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
7 months ago
jared.andrews07
▴ 30
0
votes
0
replies
385
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount
csaw
paired
12 months ago
julie.chevalier
• 0
2
votes
4
replies
1.0k
views
Error with regionCounts()
csaw
15 months ago
Chris
▴ 20
0
votes
0
replies
445
views
some questions about eliminating efficiency biaes in csaw user's guide
csawUsersGuide
csaw
16 months ago
sashu
• 0
3
votes
4
replies
1.8k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
18 months ago
spg
• 0
0
votes
0
replies
483
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma
edgeR
csaw
19 months ago • updated 18 months ago
Bogdan
▴ 670
1
vote
3
replies
1.7k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq
regionCounts
csaw
updated 7 months ago by
dineika.chandrananda
• 0 • written 2.2 years ago by
zgraytho88
• 0
1
vote
2
replies
1.3k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 2.3 years ago by
Rory Stark
★ 5.2k • written 2.3 years ago by
maria.soler
• 0
0
votes
2
replies
710
views
CSAW Users Guide Ch 4-6 are not accessible/readable
csaw
csawUsersGuide
updated 2.6 years ago by
Aaron Lun
★ 28k • written 2.6 years ago by
kimmai.phan
• 0
0
votes
1
reply
1.6k
views
[CSAW] Erreur : Negative counts not allowed
csaw
2.7 years ago
Nicolas Servant
▴ 260
3
votes
5
replies
2.7k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw
ATAC-seq
Tn5 insertions
updated 3.7 years ago by
Antonio Ahn
▴ 10 • written 3.7 years ago by
alexandre.blais
▴ 50
2
votes
1
reply
1.3k
views
normOffsets in csaw
csaw
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
ATpoint
★ 4.2k
1
vote
2
replies
1.2k
views
Error in csaw::windowCounts when using readParam
csaw
GenomeInfoDb
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
RichardJActon
▴ 50
0
votes
4
replies
1.7k
views
DiffBind or csaw between different transcription factors
DiffBind
csaw
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
GFM
▴ 20
1
vote
3
replies
1.2k
views
csaw differential binding visualization
csaw
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
C T
▴ 140
2
votes
1
reply
998
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw
chip-seq
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
ATpoint
★ 4.2k
3
votes
1
reply
1.7k
views
Correct use of TMM / normalization factors based on large bins
csaw
TMM
4.9 years ago
ATpoint
★ 4.2k
1
vote
7
replies
1.7k
views
Error while running normOffsets in diffhic
diffhic
csaw
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 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 5.0 years ago by
Martin Morgan
25k • written 5.0 years ago by
vanbelj
▴ 30
3
votes
7
replies
3.9k
views
DEseq2 for differential binding analysis ChIP seq
deseq2
diffbind
csaw
greylistchip
chipseq
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
Yonatan Amzaleg
• 0
0
votes
7
replies
1.4k
views
A problem with csaw that I don't think is a problem with csaw
csaw
caught segfault
5.6 years ago
sorjuelal
• 0
0
votes
4
replies
1.5k
views
csaw spike-in normalization
ChIP-seq
csaw
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Nicolas Servant
▴ 260
0
votes
1
reply
890
views
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma
csaw
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
gabriel.hoffman
▴ 130
1
vote
3
replies
1.4k
views
CSAW ready to use R script
csaw
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
polaxgr
▴ 10
0
votes
1
reply
1.3k
views
Best csaw normalization approach for ATAC-seq data
csaw
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
Lucy
▴ 60
0
votes
2
replies
1.0k
views
csaw: how to hack filtering windows by negative input controls?
csaw
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
Jenny Drnevich
★ 2.0k
2
votes
5
replies
1.2k
views
Differential ChIP-seq analysis
diffbind
csaw
updated 6.0 years ago by
Rory Stark
★ 5.2k • written 6.0 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 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
94133
• 0
2
votes
2
replies
1.1k
views
csaw: Estimate fragment length
csaw
6.3 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 6.7 years ago by
Martin Morgan
25k • written 6.7 years ago by
favorov
• 0
3
votes
7
replies
2.1k
views
complex design for chip-seq analysis
chipseq
csaw
limma
design matrix
multiple factor design
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
Assa Yeroslaviz
★ 1.5k
1
vote
2
replies
1.0k
views
the Normalise function in csaw
csaw
6.7 years ago
tangj
▴ 10
0
votes
2
replies
1.3k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw
histone chip-seq
chip-seq
updated 6.8 years ago by
Aaron Lun
★ 28k • written 6.8 years ago by
gil.hornung
• 0
2
votes
2
replies
1.2k
views
csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
csaw
updated 6.8 years ago by
Aaron Lun
★ 28k • written 6.8 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 6.8 years ago by
Aaron Lun
★ 28k • written 6.8 years ago by
zhangly811
• 0
3
votes
11
replies
2.4k
views
Exporting normalized counts over final DB windows from csaw
csaw
edger
chip-seq
updated 6.9 years ago by
Ryan C. Thompson
★ 7.9k • written 6.9 years ago by
jms1223
▴ 10
1
vote
2
replies
1.3k
views
csaw : effect of library size on filtering of uninteresting windows
csaw
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
Vivek.b
▴ 100
2
votes
2
replies
965
views
Run windowCounts only on annotated regions?
csaw
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 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 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
jma1991
▴ 70
3
votes
6
replies
1.9k
views
Differential Pol2 pausing analysis
edger
csaw
chipseq
differential binding analysis
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
dalerr
• 0
3
votes
3
replies
1.6k
views
Use csaw to build matrix for heatmap?
csaw
chipseq
edger
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
jmKeith
• 0
3
votes
4
replies
2.0k
views
Interpretation of cross correlation plot to determine fragment length
csaw
chip-seq
histone
updated 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 years ago by
siklenkak
• 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 7.7 years ago by
Aaron Lun
★ 28k • written 7.7 years ago by
s1437643
▴ 20
2
votes
11
replies
1.9k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
7.8 years ago
endrebak85
▴ 40
2
votes
2
replies
1.2k
views
csaw: removing PCR duplicates using dedup flag
csaw
dedup
updated 7.8 years ago by
James W. MacDonald
66k • written 7.8 years ago by
asif.zubair
• 0
2
votes
1
reply
1.9k
views
csaw with negative controls
csaw
8.0 years ago
chriad
▴ 10
5
votes
6
replies
2.0k
views
Getting normalized read counts from region counts
regionCounts
TMM
csaw
8.1 years ago
saadmurtazakhan
▴ 10
1
vote
18
replies
3.4k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq
TSS
TMM
csaw
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 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 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
chriad
▴ 10
3
votes
1
reply
1.4k
views
window counts in csaw
csaw
counts
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
nobishvarghese
• 0
50 results • Page
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Replies
Comment: limma comparison for small sample size and how to get covariance matrix
by
Gordon Smyth
51k
Your MDS plot is better than before, but you are still not following the recommendation for making for making such plots given in the limma…
Comment: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
Also, ``` > result <- mapUniProt( from = "EMBL-GenBank-DDBJ_CDS", to = "UniProtKB", query = c("ACF95883.1") ) > result From…
Comment: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
Ugh, here's the link https://www.uniprot.org/id-mapping/uniprotkb/dd08aa16774d98ef087dc3bd708582012bba49e2/overview?fields=accession%2Cre…
Answer: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
The input should be 'EMBL-GenBank-DDBJ_CDS", as that is a GenBank ID.
Answer: XCMS2 of orbitrap data
by
Elodie
• 0
Hi, I have the same question, I have acquired MS2 data with PRM analysis and inclusion lists of several ions. I have a list of product ion…
Votes
Answer: EPIC array hg38 annotation?
Answer: Why does DESeq2 give negative log2 fold change in treatment vs control for some
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
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