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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
6
votes
8
replies
1.2k
views
CAGEr bug report: wrong consensus cluster results
CAGEr
updated 9 months ago by
Charles Plessy
▴ 180 • written 16 months ago by
Meng
▴ 30
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
4
votes
5
replies
1.2k
views
no import.bam function in CAGEr version 1.22.3
cager
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
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 2.4 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
5.5 years ago
Pengcheng Yang
▴ 60
1
vote
4
replies
815
views
CAGEr quantilePositions() takes forever to run
CAGEr
quantilePositions
3.9 years ago
mirkocelii
▴ 40
1
vote
2
replies
822
views
CAGEexp vs CAGErseq
CAGEr
updated 2.5 years ago by
Charles Plessy
▴ 180 • written 3.0 years ago by
MatteoP
▴ 10
1
vote
1
reply
988
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
1
vote
1
reply
868
views
CAGEr: consensusCluster doesn't have dominant CTSS info
cager
5.9 years ago
Jingwen
▴ 10
1
vote
3
replies
837
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
900
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 9.7 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
0
votes
1
reply
897
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 2.6 years ago by
Charles
• 0 • written 3.6 years ago by
leehami7407
• 0
0
votes
0
replies
463
views
CAGEr consensusClustersDESeq2()
CAGEr
3.0 years ago
MatteoP
▴ 10
0
votes
3
replies
952
views
CAGEr: Problem when running getCTSS
CAGEr
updated 2.5 years ago by
Charles Plessy
▴ 180 • written 2.6 years ago by
Sergio
• 0
21 results • Page
1 of 1
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Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
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