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CAGEr
•
reset
9
votes
18
replies
2.3k
views
bam2CTSS function error from CAGEr package
cager
5.5 years ago
Pengcheng Yang
▴ 60
4
votes
5
replies
2.1k
views
CAGEr : problem while filtering the bamFile
CAGEr
cage
updated 2.6 years ago by
jingxian.18
• 0 • written 8.2 years ago by
Vivek.b
▴ 100
2
votes
8
replies
2.0k
views
CAGEr BAM files size issue
CAGEr
BAM
software error
R
biostrings
updated 6.7 years ago by
Charles Plessy
▴ 180 • written 6.8 years ago by
orzechowska.mag
▴ 10
1
vote
2
replies
1.3k
views
error: getCTSS from CAGEexp class with removeFirstG=TRUE
cager
5.5 years ago
Pengcheng Yang
▴ 60
2
votes
5
replies
1.3k
views
Does `clusterCTSS` and `aggregateTagClusters` sum raw-tag counts (and tpm) of the clustered tags into the resultant cluster?
CTSS clustering
tag per million
tag counts
CAGEr
updated 2.4 years ago by
Charles Plessy
▴ 180 • written 4.9 years ago by
regcastillo1990
• 0
1
vote
6
replies
1.2k
views
Behaviour of getCTSS on a CAGEset - extra reads?
cager
cage
ctss
updated 4.0 years ago by
Charles Plessy
▴ 180 • written 4.8 years ago by
sarac
▴ 20
6
votes
8
replies
1.2k
views
CAGEr bug report: wrong consensus cluster results
CAGEr
updated 9 months ago by
Charles Plessy
▴ 180 • written 17 months ago by
Meng
▴ 30
4
votes
5
replies
1.2k
views
no import.bam function in CAGEr version 1.22.3
cager
5.6 years ago • updated 5.5 years ago
Pengcheng Yang
▴ 60
4
votes
6
replies
1.1k
views
CAGEr - Error with aggregateTagClusters() - invalid class IRanges object: width(x) cannot contain negative integers
CAGEr
IRanges
aggregateTagClusters
4.0 years ago
mirkocelii
▴ 40
0
votes
5
replies
1.1k
views
CAGEr promoter width graph
CAGEr
updated 2.6 years ago by
Charles
• 0 • written 3.6 years ago by
leehami7407
• 0
0
votes
1
reply
1.1k
views
CAGEr - How to change plot axis range in CAGEr
BRAIN
CAGEr
BRAIN
CAGEr
updated 6.0 years ago by
Charles Plessy
▴ 180 • written 9.7 years ago by
Tobias Hohenauer
▴ 10
0
votes
1
reply
1.1k
views
Scale Y-axis in "plotInterquantileWidth" function for an easier comparison between conditions
CAGEr
updated 9.2 years ago by
James W. MacDonald
65k • written 9.2 years ago by
calibula2000
• 0
1
vote
1
reply
992
views
clusterCTSS() error when running CAGEr
CAGEr
updated 6.5 years ago by
Charles Plessy
▴ 180 • written 6.5 years ago by
bo_yan
▴ 10
0
votes
3
replies
956
views
CAGEr: Problem when running getCTSS
CAGEr
updated 2.5 years ago by
Charles Plessy
▴ 180 • written 2.6 years ago by
Sergio
• 0
0
votes
0
replies
902
views
CAGEr get TSS in bed file
TSS
promoter
cage
cager
5.4 years ago
bharata1803
▴ 60
0
votes
1
reply
900
views
a problem from import CTSStable in CAGEr
cager
CAGEr
5.5 years ago
Zhong JW
• 0
1
vote
1
reply
870
views
CAGEr: consensusCluster doesn't have dominant CTSS info
cager
5.9 years ago
Jingwen
▴ 10
1
vote
3
replies
843
views
CAGEr: Quantile Values (q_0.1 and q_0.9) in CAGEset / CAGEexp objects
CAGEr
CAGEset
quantile
CAGEexp
4.0 years ago
mirkocelii
▴ 40
1
vote
2
replies
825
views
CAGEexp vs CAGErseq
CAGEr
updated 2.5 years ago by
Charles Plessy
▴ 180 • written 3.0 years ago by
MatteoP
▴ 10
1
vote
4
replies
817
views
CAGEr quantilePositions() takes forever to run
CAGEr
quantilePositions
3.9 years ago
mirkocelii
▴ 40
0
votes
0
replies
468
views
CAGEr consensusClustersDESeq2()
CAGEr
3.0 years ago
MatteoP
▴ 10
21 results • Page
1 of 1
Recent ...
Replies
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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