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Csaw
•
reset
1
vote
18
replies
4.3k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq
TSS
TMM
csaw
updated 9.3 years ago by
Aaron Lun
★ 29k • written 9.3 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 9.4 years ago by
Aaron Lun
★ 29k • written 9.4 years ago by
chriad
▴ 10
3
votes
1
reply
1.7k
views
window counts in csaw
csaw
counts
updated 9.4 years ago by
Aaron Lun
★ 29k • written 9.4 years ago by
nobishvarghese
• 0
2
votes
1
reply
1.3k
views
How does csaw handle multiply aligned reads?
csaw
chip-seq
updated 9.4 years ago by
Aaron Lun
★ 29k • written 9.4 years ago by
endrebak85
▴ 40
1
vote
3
replies
1.4k
views
csaw: dumpPE on multiple bam files.
csaw
dumpPE
windowCounts
9.8 years ago • updated 9.4 years ago
asif.zubair
• 0
1
vote
1
reply
1.2k
views
csaw: post clustering description of regions
csaw
mergeWindows
updated 9.4 years ago by
Aaron Lun
★ 29k • written 9.4 years ago by
asif.zubair
• 0
3
votes
2
replies
1.5k
views
csaw: when not to dedup
csaw
dedup
updated 4.1 years ago by
uli.arb
• 0 • written 9.4 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 9.4 years ago by
Aaron Lun
★ 29k • written 9.4 years ago by
nobishvarghese
• 0
4
votes
1
reply
3.5k
views
csaw - workflow to incorporate input/control samples?
csaw
chipseq
differential binding analysis
updated 9.4 years ago by
Aaron Lun
★ 29k • written 9.4 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 9.4 years ago by
Aaron Lun
★ 29k • written 9.4 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 9.4 years ago by
Aaron Lun
★ 29k • written 9.4 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 9.5 years ago by
Aaron Lun
★ 29k • written 9.5 years ago by
Amitha Sampath
▴ 10
2
votes
2
replies
1.6k
views
CSAW : at which bam files are corresponding “up” regions
csaw
up regions
bam file
gain and loss of enrichment
updated 9.5 years ago by
Aaron Lun
★ 29k • written 9.5 years ago by
JoannaF
▴ 10
2
votes
7
replies
1.9k
views
CSAW: GAIN and LOSS of enrichment
csaw
updated 9.5 years ago by
JoannaF
▴ 10 • written 10.4 years ago by
sergio.espeso-gil
• 0
6
votes
2
replies
1.6k
views
Saving the CSAW results to file
edger
csaw
updated 9.8 years ago by
Aaron Lun
★ 29k • written 9.8 years ago by
gthm
▴ 30
0
votes
5
replies
2.2k
views
CSAW: Error: could not find function "normOffsets"
csaw
edgeR
chipseq
updated 9.8 years ago by
Aaron Lun
★ 29k • written 9.8 years ago by
gthm
▴ 30
1
vote
1
reply
1.4k
views
FDR calculation by combineTests in csaw
csaw
updated 9.9 years ago by
Aaron Lun
★ 29k • written 9.9 years ago by
renanec
▴ 20
2
votes
1
reply
867
views
csaw not up to date
csaw
updated 9.9 years ago by
Aaron Lun
★ 29k • written 9.9 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
9.9 years ago
Pierre-François Roux
• 0
2
votes
3
replies
1.2k
views
CSAW: getBestTest p-value
csaw
updated 10.0 years ago by
Gordon Smyth
53k • written 10.0 years ago by
sergio.espeso-gil
• 0
2
votes
7
replies
1.8k
views
CSAW: Annotation through clustering with external information
csaw
updated 10.1 years ago by
Gordon Smyth
53k • written 10.1 years ago by
sergio.espeso-gil
• 0
1
vote
1
reply
1.2k
views
csaw: input coverage RleLists instead of bam files
csaw
updated 10.2 years ago by
Aaron Lun
★ 29k • written 10.2 years ago by
Arne Muller
▴ 20
1
vote
7
replies
1.5k
views
CSAW: filtering prior information
csaw
10.3 years ago
sergio.espeso-gil
• 0
3
votes
2
replies
3.9k
views
TMM normalisation method
Csaw
csaw
10.5 years ago
sergio.espeso-gil
• 0
4
votes
4
replies
2.1k
views
Strand-aware CSAW analysis
csaw
chip-seq
clip-seq
10.6 years ago
IV
▴ 30
75 results • Page
2 of 2
Recent ...
Replies
Comment: Sharing a collection of datasets in ExperimentHub
by
Peter Hickey
▴ 760
The [**scRNAseq**](https://bioconductor.org/packages/scRNAseq/) package ([source on GitHub](https://github.com/LTLA/scRNAseq)) might serve …
Answer: EuroBioC2023 abstract submission is open!
by
efuite222
• 0
Abstract submissions are now open for the #EuroBioC2023 conference in Ghent, Belgium, from September 20-22; submit by April 14 for opportu…
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
by
ReinholdGaylord99
• 0
Thank you so much! https://www.nature.com/articles/s41467-021-25960-2/ [geometry dash lite](https://geometrydashlite.online)
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
Gordon Smyth
53k
I'm not sure that I understand. You have a dataset that, even after pseudo-bulking, still has 6000 samples? That is surprising. Retaining …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
abaed
• 0
Hello again @gordonsmyth, I've now applied the analysis using a more detailed annotation of cell types/clusters, which includes about 100 …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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