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Showing :
csaw
•
reset
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
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
2
votes
11
replies
1.9k
views
csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
csaw
7.6 years ago
endrebak85
▴ 40
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
2
votes
7
replies
1.3k
views
CSAW: Annotation through clustering with external information
csaw
updated 8.7 years ago by
Gordon Smyth
50k • written 8.7 years ago by
sergio.espeso-gil
• 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
2
votes
7
replies
1.5k
views
CSAW: GAIN and LOSS of enrichment
csaw
updated 8.1 years ago by
JoannaF
▴ 10 • written 9.0 years ago by
sergio.espeso-gil
• 0
1
vote
7
replies
1.2k
views
CSAW: filtering prior information
csaw
8.9 years ago
sergio.espeso-gil
• 0
1
vote
7
replies
1.7k
views
Error while running normOffsets in diffhic
diffhic
csaw
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
shopnil99
• 0
3
votes
7
replies
3.8k
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
5
votes
6
replies
2.0k
views
Getting normalized read counts from region counts
regionCounts
TMM
csaw
7.9 years ago
saadmurtazakhan
▴ 10
3
votes
6
replies
1.9k
views
Differential Pol2 pausing analysis
edger
csaw
chipseq
differential binding analysis
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
dalerr
• 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 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
94133
• 0
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
1.8k
views
CSAW: Error: could not find function "normOffsets"
csaw
edgeR
chipseq
updated 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 years ago by
gthm
▴ 30
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 3.6 years ago by
alexandre.blais
▴ 50
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
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
2
votes
4
replies
925
views
Error with regionCounts()
csaw
13 months ago
Chris
• 0
4
votes
4
replies
1.6k
views
Strand-aware CSAW analysis
csaw
chip-seq
clip-seq
9.2 years ago
IV
▴ 30
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
4
replies
1.7k
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
2
votes
3
replies
1.2k
views
Unexpected reversal in normalization factors from csaw
csaw
normalization
updated 8.0 years ago by
Aaron Lun
★ 28k • written 8.0 years ago by
Ryan C. Thompson
★ 7.9k
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 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
zhangly811
• 0
1
vote
3
replies
1.6k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq
regionCounts
csaw
updated 5 months ago by
dineika.chandrananda
• 0 • written 2.0 years ago by
zgraytho88
• 0
1
vote
3
replies
1.1k
views
csaw: dumpPE on multiple bam files.
csaw
dumpPE
windowCounts
8.5 years ago • updated 8.0 years ago
asif.zubair
• 0
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
3
replies
1.6k
views
Use csaw to build matrix for heatmap?
csaw
chipseq
edger
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
jmKeith
• 0
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
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
1
vote
3
replies
1.3k
views
CSAW ready to use R script
csaw
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
polaxgr
▴ 10
2
votes
3
replies
945
views
CSAW: getBestTest p-value
csaw
updated 8.6 years ago by
Gordon Smyth
50k • written 8.6 years ago by
sergio.espeso-gil
• 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
3
votes
2
replies
3.5k
views
TMM normalisation method
Csaw
csaw
9.1 years ago
sergio.espeso-gil
• 0
4
votes
2
replies
1.4k
views
Csaw : filter windows based on matched negative control
csaw
differential binding analysis
8.5 years ago
Pierre-François Roux
• 0
6
votes
2
replies
1.3k
views
Saving the CSAW results to file
edger
csaw
updated 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 years ago by
gthm
▴ 30
2
votes
2
replies
1.3k
views
CSAW : at which bam files are corresponding “up” regions
csaw
up regions
bam file
gain and loss of enrichment
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
JoannaF
▴ 10
3
votes
2
replies
1.1k
views
csaw: when not to dedup
csaw
dedup
updated 2.7 years ago by
uli.arb
• 0 • written 8.0 years ago by
asif.zubair
• 0
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
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 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
s1437643
▴ 20
2
votes
2
replies
936
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
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
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
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
1
vote
2
replies
995
views
the Normalise function in csaw
csaw
6.6 years ago
tangj
▴ 10
2
votes
2
replies
1.1k
views
csaw: Estimate fragment length
csaw
6.2 years ago
nicolas.descostes
▴ 20
0
votes
2
replies
993
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
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
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
2
replies
665
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
50 results • Page
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Recent ...
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Hervé Pagès
16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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