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cager
•
reset
9
votes
18
replies
2.3k
views
bam2CTSS function error from CAGEr package
cager
5.6 years ago
Pengcheng Yang
▴ 60
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
2.1k
views
CAGEr : problem while filtering the bamFile
CAGEr
cage
updated 2.7 years ago by
jingxian.18
• 0 • written 8.2 years ago by
Vivek.b
▴ 100
4
votes
5
replies
1.2k
views
no import.bam function in CAGEr version 1.22.3
cager
5.6 years ago
Pengcheng Yang
▴ 60
4
votes
6
replies
1.2k
views
CAGEr - Error with aggregateTagClusters() - invalid class IRanges object: width(x) cannot contain negative integers
CAGEr
IRanges
aggregateTagClusters
4.0 years ago
mirkocelii
▴ 40
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
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 2.5 years ago by
Charles Plessy
▴ 180 • written 4.9 years ago by
regcastillo1990
• 0
1
vote
2
replies
1.3k
views
error: getCTSS from CAGEexp class with removeFirstG=TRUE
cager
5.6 years ago
Pengcheng Yang
▴ 60
1
vote
4
replies
832
views
CAGEr quantilePositions() takes forever to run
CAGEr
quantilePositions
4.0 years ago
mirkocelii
▴ 40
1
vote
2
replies
837
views
CAGEexp vs CAGErseq
CAGEr
updated 2.5 years ago by
Charles Plessy
▴ 180 • written 3.1 years ago by
MatteoP
▴ 10
1
vote
1
reply
1.0k
views
clusterCTSS() error when running CAGEr
CAGEr
updated 6.6 years ago by
Charles Plessy
▴ 180 • written 6.6 years ago by
bo_yan
▴ 10
1
vote
1
reply
878
views
CAGEr: consensusCluster doesn't have dominant CTSS info
cager
5.9 years ago
Jingwen
▴ 10
1
vote
3
replies
852
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
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
0
votes
0
replies
909
views
CAGEr get TSS in bed file
TSS
promoter
cage
cager
5.4 years ago
bharata1803
▴ 60
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 9.8 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 9.3 years ago by
James W. MacDonald
65k • written 9.3 years ago by
calibula2000
• 0
0
votes
1
reply
908
views
a problem from import CTSStable in CAGEr
cager
CAGEr
5.5 years ago
Zhong JW
• 0
0
votes
5
replies
1.1k
views
CAGEr promoter width graph
CAGEr
updated 2.7 years ago by
Charles
• 0 • written 3.6 years ago by
leehami7407
• 0
0
votes
0
replies
473
views
CAGEr consensusClustersDESeq2()
CAGEr
3.1 years ago
MatteoP
▴ 10
0
votes
3
replies
962
views
CAGEr: Problem when running getCTSS
CAGEr
updated 2.5 years ago by
Charles Plessy
▴ 180 • written 2.7 years ago by
Sergio
• 0
21 results • Page
1 of 1
Recent ...
Replies
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…
Comment: Help with running egsea()
by
James W. MacDonald
65k
I don't understand the last question, but do look at the msigdb.gsets argument to `buildIdx` in the help page for that function.
Votes
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Answer: How to save the DEXSeq results
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