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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
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
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
5.6 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 2.5 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
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
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
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
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
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
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
908
views
a problem from import CTSStable in CAGEr
cager
CAGEr
5.5 years ago
Zhong JW
• 0
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
850
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
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
4
replies
831
views
CAGEr quantilePositions() takes forever to run
CAGEr
quantilePositions
4.0 years ago
mirkocelii
▴ 40
0
votes
0
replies
473
views
CAGEr consensusClustersDESeq2()
CAGEr
3.1 years ago
MatteoP
▴ 10
21 results • Page
1 of 1
Recent ...
Replies
Comment: Couldn't connect to server while using "pathways"
by
Michael Love
41k
You've put the tag "DESeq2" which results in an email to the maintainer, me, that I should respond to a post on the support site. Can you …
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Vincent J. Carey, Jr.
6.7k
btw that was run on M1 mac
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Vincent J. Carey, Jr.
6.7k
the test is not portable > aa <- aa_mutmat(acc = "MIYS930101", aaindex = "aaindex2") > str(aa) num [1:20, 1:20] 0.34 -0.0…
Comment: Method to find pathways different between 2 groups
by
Chris
• 0
Sorry for not clear. I just try to find papers use this method for learning purpose. Which gives more context and detail examples, so I may…
Comment: Improving the design matrices vignette in RNAseq123
by
Lluís Revilla Sancho
▴ 730
Cool. Thanks for looking into it.
Votes
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
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