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cager
•
reset
9
votes
18
replies
3.4k
views
bam2CTSS function error from CAGEr package
cager
7.3 years ago
Pengcheng Yang
▴ 60
6
votes
8
replies
2.1k
views
CAGEr bug report: wrong consensus cluster results
CAGEr
updated 2.5 years ago by
Charles Plessy
▴ 180 • written 3.1 years ago by
Meng
▴ 30
2
votes
8
replies
2.8k
views
CAGEr BAM files size issue
CAGEr
BAM
software error
R
biostrings
updated 8.5 years ago by
Charles Plessy
▴ 180 • written 8.5 years ago by
orzechowska.mag
▴ 10
1
vote
6
replies
2.0k
views
Behaviour of getCTSS on a CAGEset - extra reads?
cager
cage
ctss
updated 5.7 years ago by
Charles Plessy
▴ 180 • written 6.5 years ago by
sarac
▴ 20
4
votes
6
replies
1.9k
views
CAGEr - Error with aggregateTagClusters() - invalid class IRanges object: width(x) cannot contain negative integers
CAGEr
IRanges
aggregateTagClusters
5.7 years ago
mirkocelii
▴ 40
2
votes
5
replies
2.0k
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 4.2 years ago by
Charles Plessy
▴ 180 • written 6.6 years ago by
regcastillo1990
• 0
4
votes
5
replies
2.8k
views
CAGEr : problem while filtering the bamFile
CAGEr
cage
updated 4.4 years ago by
jingxian.18
• 0 • written 9.9 years ago by
Vivek.b
▴ 100
4
votes
5
replies
1.8k
views
no import.bam function in CAGEr version 1.22.3
cager
7.3 years ago
Pengcheng Yang
▴ 60
0
votes
5
replies
1.7k
views
CAGEr promoter width graph
CAGEr
updated 4.4 years ago by
Charles
• 0 • written 5.3 years ago by
leehami7407
• 0
1
vote
4
replies
1.4k
views
CAGEr quantilePositions() takes forever to run
CAGEr
quantilePositions
5.7 years ago
mirkocelii
▴ 40
0
votes
3
replies
1.5k
views
CAGEr: Problem when running getCTSS
CAGEr
updated 4.2 years ago by
Charles Plessy
▴ 180 • written 4.4 years ago by
Sergio
• 0
1
vote
3
replies
1.4k
views
CAGEr: Quantile Values (q_0.1 and q_0.9) in CAGEset / CAGEexp objects
CAGEr
CAGEset
quantile
CAGEexp
5.7 years ago
mirkocelii
▴ 40
1
vote
2
replies
1.8k
views
error: getCTSS from CAGEexp class with removeFirstG=TRUE
cager
7.3 years ago
Pengcheng Yang
▴ 60
1
vote
2
replies
1.3k
views
CAGEexp vs CAGErseq
CAGEr
updated 4.2 years ago by
Charles Plessy
▴ 180 • written 4.8 years ago by
MatteoP
▴ 10
1
vote
1
reply
1.3k
views
CAGEr: consensusCluster doesn't have dominant CTSS info
cager
7.7 years ago
Jingwen
▴ 10
0
votes
1
reply
1.5k
views
CAGEr - How to change plot axis range in CAGEr
BRAIN
CAGEr
BRAIN
CAGEr
updated 7.7 years ago by
Charles Plessy
▴ 180 • written 11.5 years ago by
Tobias Hohenauer
▴ 10
1
vote
1
reply
1.5k
views
clusterCTSS() error when running CAGEr
CAGEr
updated 8.3 years ago by
Charles Plessy
▴ 180 • written 8.3 years ago by
bo_yan
▴ 10
0
votes
1
reply
1.4k
views
Scale Y-axis in "plotInterquantileWidth" function for an easier comparison between conditions
CAGEr
updated 11.0 years ago by
James W. MacDonald
68k • written 11.0 years ago by
calibula2000
• 0
0
votes
1
reply
1.3k
views
a problem from import CTSStable in CAGEr
cager
CAGEr
7.2 years ago
Zhong JW
• 0
0
votes
0
replies
758
views
CAGEr consensusClustersDESeq2()
CAGEr
4.8 years ago
MatteoP
▴ 10
0
votes
0
replies
1.4k
views
CAGEr get TSS in bed file
TSS
promoter
cage
cager
7.2 years ago
bharata1803
▴ 60
0
votes
0
replies
41
views
Spam:
Can I cancel my British Airways flight and get a refund?
CAGEr
gep2pep
hcg110.db
10 months ago
Haggu
10
22 results • Page
1 of 1
Recent ...
Replies
Comment: Combining two proteomics datasets with limpa
by
Andrew Pattison
• 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Julia Broadbent
• 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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