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csaw
•
reset
1
vote
18
replies
4.4k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq
TSS
TMM
csaw
updated 9.5 years ago by
Aaron Lun
★ 29k • written 9.5 years ago by
saadmurtazakhan
▴ 10
1
vote
3
replies
2.2k
views
csaw filterWindows function results in a warning: ("Zero library size detected.")
csaw
updated 9.6 years ago by
Aaron Lun
★ 29k • written 9.6 years ago by
chriad
▴ 10
3
votes
1
reply
1.7k
views
window counts in csaw
csaw
counts
updated 9.6 years ago by
Aaron Lun
★ 29k • written 9.6 years ago by
nobishvarghese
• 0
2
votes
1
reply
1.3k
views
How does csaw handle multiply aligned reads?
csaw
chip-seq
updated 9.6 years ago by
Aaron Lun
★ 29k • written 9.6 years ago by
endrebak85
▴ 40
1
vote
3
replies
1.5k
views
csaw: dumpPE on multiple bam files.
csaw
dumpPE
windowCounts
10.0 years ago • updated 9.6 years ago
asif.zubair
• 0
1
vote
1
reply
1.2k
views
csaw: post clustering description of regions
csaw
mergeWindows
updated 9.6 years ago by
Aaron Lun
★ 29k • written 9.6 years ago by
asif.zubair
• 0
3
votes
2
replies
1.6k
views
csaw: when not to dedup
csaw
dedup
updated 4.3 years ago by
uli.arb
• 0 • written 9.6 years ago by
asif.zubair
• 0
3
votes
1
reply
1.1k
views
Detection of methylated regions from MeDIP data using csaw
csaw
medip-chip
updated 9.6 years ago by
Aaron Lun
★ 29k • written 9.6 years ago by
nobishvarghese
• 0
4
votes
1
reply
3.6k
views
csaw - workflow to incorporate input/control samples?
csaw
chipseq
differential binding analysis
updated 9.6 years ago by
Aaron Lun
★ 29k • written 9.6 years ago by
markus.ringner
▴ 10
2
votes
1
reply
1.8k
views
Strategy for choosing window size and read extension length for csaw?
csaw
differential binding analysis
bin size
updated 9.6 years ago by
Aaron Lun
★ 29k • written 9.6 years ago by
Ryan C. Thompson
★ 7.9k
2
votes
3
replies
1.5k
views
Unexpected reversal in normalization factors from csaw
csaw
normalization
updated 9.6 years ago by
Aaron Lun
★ 29k • written 9.6 years ago by
Ryan C. Thompson
★ 7.9k
1
vote
1
reply
1.9k
views
Differential binding using csaw
csaw
differential binding analysis
chipseq
differential expression
differential gene expression
updated 9.7 years ago by
Aaron Lun
★ 29k • written 9.7 years ago by
Amitha Sampath
▴ 10
2
votes
2
replies
1.7k
views
CSAW : at which bam files are corresponding “up” regions
csaw
up regions
bam file
gain and loss of enrichment
updated 9.7 years ago by
Aaron Lun
★ 29k • written 9.7 years ago by
JoannaF
▴ 10
2
votes
7
replies
1.9k
views
CSAW: GAIN and LOSS of enrichment
csaw
updated 9.7 years ago by
JoannaF
▴ 10 • written 10.6 years ago by
sergio.espeso-gil
• 0
6
votes
2
replies
1.7k
views
Saving the CSAW results to file
edger
csaw
updated 10.0 years ago by
Aaron Lun
★ 29k • written 10.0 years ago by
gthm
▴ 30
0
votes
5
replies
2.2k
views
CSAW: Error: could not find function "normOffsets"
csaw
edgeR
chipseq
updated 10.0 years ago by
Aaron Lun
★ 29k • written 10.0 years ago by
gthm
▴ 30
1
vote
1
reply
1.4k
views
FDR calculation by combineTests in csaw
csaw
updated 10.0 years ago by
Aaron Lun
★ 29k • written 10.0 years ago by
renanec
▴ 20
2
votes
1
reply
898
views
csaw not up to date
csaw
updated 10.1 years ago by
Aaron Lun
★ 29k • written 10.1 years ago by
jerome.eeckhoute
• 0
4
votes
2
replies
1.8k
views
Csaw : filter windows based on matched negative control
csaw
differential binding analysis
10.1 years ago
Pierre-François Roux
• 0
2
votes
3
replies
1.3k
views
CSAW: getBestTest p-value
csaw
updated 10.2 years ago by
Gordon Smyth
53k • written 10.2 years ago by
sergio.espeso-gil
• 0
2
votes
7
replies
1.8k
views
CSAW: Annotation through clustering with external information
csaw
updated 10.3 years ago by
Gordon Smyth
53k • written 10.3 years ago by
sergio.espeso-gil
• 0
1
vote
1
reply
1.2k
views
csaw: input coverage RleLists instead of bam files
csaw
updated 10.4 years ago by
Aaron Lun
★ 29k • written 10.4 years ago by
Arne Muller
▴ 20
1
vote
7
replies
1.6k
views
CSAW: filtering prior information
csaw
10.5 years ago
sergio.espeso-gil
• 0
3
votes
2
replies
3.9k
views
TMM normalisation method
Csaw
csaw
10.7 years ago
sergio.espeso-gil
• 0
4
votes
4
replies
2.1k
views
Strand-aware CSAW analysis
csaw
chip-seq
clip-seq
10.8 years ago
IV
▴ 30
75 results • Page
2 of 2
Recent ...
Replies
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
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
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★ 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/
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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