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drimseq
•
reset
1
vote
1
reply
674
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
15 months ago
NiKo
▴ 10
0
votes
0
replies
577
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq
DRIMSeq
22 months ago
Luca
• 0
0
votes
3
replies
962
views
DRIMseq error for paired sample analysis
DRIMSeq
22 months ago • updated 21 months ago
Luca
• 0
2
votes
2
replies
932
views
Inconsistent Dirichlet-multinominal coefficient and Beta-Binominal coefficient for a transcript in DTU analysis.
rnaseqDTU
DRIMSeq
2.5 years ago
wangziwei0010
▴ 10
0
votes
4
replies
2.0k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq
DRIMSeq
updated 2.7 years ago by
jeroen.gilis
▴ 90 • written 2.7 years ago by
phoebe1354
• 0
0
votes
5
replies
1.6k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
3.5 years ago • updated 3.4 years ago
bioinformatic_trainee
▴ 10
3
votes
4
replies
1.5k
views
DRIMSeq: many NAs in results compared to DESeq2 ?
DESeq2
DRIMSeq
dtu
RNASeq
3.5 years ago
sbcn
▴ 80
0
votes
0
replies
1.1k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
3.8 years ago
jbono
▴ 10
0
votes
2
replies
1.3k
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
3.9 years ago • updated 3.8 years ago
Gaia
• 0
0
votes
5
replies
1.8k
views
Error using DRIMSeq with Salmon count data
DRIMSeq
tximport
txdb
Salmon
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
Charlotte
• 0
1
vote
1
reply
1.0k
views
Error in dmTest() from DRIMSeq package - tuQTL
DRIMSeq
tuQTL
updated 4.5 years ago by
Gosia Nowicka
▴ 90 • written 4.5 years ago by
iaradsouza1
• 0
0
votes
5
replies
1.4k
views
DRIMSeq with technical replicates
DRIMSeq
R
DTU
technical replicates
deseq2
updated 4.5 years ago by
Kevin Blighe
★ 4.0k • written 4.5 years ago by
poecile.pal
• 0
1
vote
1
reply
996
views
DEXSeq-DTU normalisation suggestion - scaledTPM vs dtuScaledTPM
tximport
DEXSeq-DTU
DRIMSeq
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
aleksandar.baburski.g
• 0
0
votes
0
replies
848
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq
DRIMSeq
4.7 years ago
alexis.weinreb
• 0
0
votes
11
replies
1.9k
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU
DRIMseq
DEXseq
rna-seq
5.8 years ago
saddamhusain77
• 0
0
votes
1
reply
1.0k
views
stageR with input from DRIMSeq
DRIMSeq
stageR
updated 5.9 years ago by
Koen Van den Berge
▴ 180 • written 5.9 years ago by
sdvie
• 0
1
vote
2
replies
1.7k
views
Normalized transcript/exon counts for network analysis
drimseq
dexseq
wgcna
sva
updated 5.9 years ago by
Gosia Nowicka
▴ 90 • written 5.9 years ago by
maya.kappil
▴ 30
0
votes
4
replies
1.8k
views
DRIMSeq continious variable in design matrix - Error during precision estimation
DRIMSeq
dmPrecision
updated 23 months ago by
Mary-Ellen
• 0 • written 6.0 years ago by
fiona.dick91
▴ 60
2
votes
4
replies
1.9k
views
stageR: Error in stageWiseAdjustment
stageR
rnaseqDTU
DRIMSeq
DEXSeq
6.0 years ago
d-joester
▴ 20
2
votes
2
replies
1.3k
views
rnaseqDTU DTU workflow - pots-hoc Filter
DTU
DRIMSeq
rnaseqDTU
updated 6.0 years ago by
Michael Love
43k • written 6.0 years ago by
fiona.dick91
▴ 60
0
votes
3
replies
1.3k
views
Post-hoc filtering on the standard deviation in proportions
drimseq
rnaseqdtu
stager
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
Jack.Hearn
• 0
1
vote
1
reply
943
views
Calling a package specific function in a for loop
drimseq
swimming downstream
for loop
sapply
updated 6.2 years ago by
Martin Morgan
25k • written 6.2 years ago by
georgewwp
• 0
4
votes
3
replies
1.7k
views
DEXSeq and DRIMSeq on paired samples?
DRIMSeq
DEXSeq
updated 6.3 years ago by
Gosia Nowicka
▴ 90 • written 6.3 years ago by
zoe.ward
• 0
2
votes
9
replies
2.1k
views
stageR NA in getAdjustedPValues() (method=dtu)
drimseq
stageR
dtu
salmon rna seq
updated 6.5 years ago by
Koen Van den Berge
▴ 180 • written 6.5 years ago by
fiona.dick91
▴ 60
1
vote
1
reply
1.4k
views
DrimSeq: installation versions
drimseq
DTU
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
somseeprags
▴ 10
1
vote
2
replies
1.8k
views
Is it possible to get Isoform-level differential isoform usage form DRIMSeq?
DRIMSeq
splicing
differential isoform usage
updated 8.0 years ago by
Gosia Nowicka
▴ 90 • written 8.0 years ago by
kristoffer.vittingseerup
▴ 20
26 results • Page
1 of 1
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Replies
Answer: Unable to find sample sheet file for ChAMP methylation data analysis
by
James W. MacDonald
67k
There is an example file in the extdata directory of the `minfiData` package that you could emulate.
Comment: Rain error: invalid annotation of time points
by
Dominik
• 0
Hi, I kept running into the same issue until I double checked their help and understood, that columns and rows have to be designed in anoth…
Answer: How to generate circular cnetplot and color nodes and edges in the same plot ?
by
Guido Hooiveld
★ 4.1k
Since the release of `enrichplot` of October 2024, the code of the function `cnetplot` has been completely rewritten by Guangchuang in orde…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza
by
mec25
• 0
I am unable to find the math behind the dba.normalize(), for instance when the E-coli fraction is used is the signal mutliplied by the fact…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA?
by
Quang NN
▴ 10
Thank you so much for taking time to provide this clarification!
Votes
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
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Martin Morgan
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Guido Hooiveld
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Joseph Fass
▴ 70
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Peter Hickey
▴ 750
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