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drimseq
•
reset
1
vote
1
reply
478
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
8 months ago
NiKo
▴ 10
0
votes
0
replies
424
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq
DRIMSeq
15 months ago
Luca
• 0
0
votes
3
replies
719
views
DRIMseq error for paired sample analysis
DRIMSeq
15 months ago
Luca
• 0
2
votes
2
replies
739
views
Inconsistent Dirichlet-multinominal coefficient and Beta-Binominal coefficient for a transcript in DTU analysis.
rnaseqDTU
DRIMSeq
24 months ago
wangziwei0010
▴ 10
0
votes
4
replies
1.6k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq
DRIMSeq
updated 2.1 years ago by
jeroen.gilis
▴ 90 • written 2.2 years ago by
phoebe1354
• 0
0
votes
5
replies
1.3k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
2.9 years ago
bioinformatic_trainee
▴ 10
3
votes
4
replies
1.2k
views
DRIMSeq: many NAs in results compared to DESeq2 ?
DESeq2
DRIMSeq
dtu
RNASeq
3.0 years ago
sbcn
▴ 80
0
votes
0
replies
912
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
3.2 years ago
jbono
▴ 10
0
votes
2
replies
1.1k
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
3.3 years ago
Gaia
• 0
0
votes
5
replies
1.5k
views
Error using DRIMSeq with Salmon count data
DRIMSeq
tximport
txdb
Salmon
updated 3.9 years ago by
Michael Love
42k • written 3.9 years ago by
Charlotte
• 0
1
vote
1
reply
835
views
Error in dmTest() from DRIMSeq package - tuQTL
DRIMSeq
tuQTL
updated 3.9 years ago by
Gosia Nowicka
▴ 90 • written 4.0 years ago by
iaradsouza1
• 0
0
votes
5
replies
1.2k
views
DRIMSeq with technical replicates
DRIMSeq
R
DTU
technical replicates
deseq2
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
poecile.pal
• 0
1
vote
1
reply
855
views
DEXSeq-DTU normalisation suggestion - scaledTPM vs dtuScaledTPM
tximport
DEXSeq-DTU
DRIMSeq
updated 4.0 years ago by
Michael Love
42k • written 4.0 years ago by
aleksandar.baburski.g
• 0
0
votes
0
replies
690
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq
DRIMSeq
4.1 years ago
alexis.weinreb
• 0
0
votes
11
replies
1.6k
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU
DRIMseq
DEXseq
rna-seq
5.2 years ago
saddamhusain77
• 0
0
votes
1
reply
861
views
stageR with input from DRIMSeq
DRIMSeq
stageR
updated 5.3 years ago by
Koen Van den Berge
▴ 180 • written 5.3 years ago by
sdvie
• 0
1
vote
2
replies
1.5k
views
Normalized transcript/exon counts for network analysis
drimseq
dexseq
wgcna
sva
updated 5.4 years ago by
Gosia Nowicka
▴ 90 • written 5.4 years ago by
maya.kappil
▴ 30
0
votes
4
replies
1.5k
views
DRIMSeq continious variable in design matrix - Error during precision estimation
DRIMSeq
dmPrecision
updated 16 months ago by
Mary-Ellen
• 0 • written 5.4 years ago by
fiona.dick91
▴ 60
2
votes
4
replies
1.7k
views
stageR: Error in stageWiseAdjustment
stageR
rnaseqDTU
DRIMSeq
DEXSeq
5.4 years ago
d-joester
▴ 20
2
votes
2
replies
1.2k
views
rnaseqDTU DTU workflow - pots-hoc Filter
DTU
DRIMSeq
rnaseqDTU
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
fiona.dick91
▴ 60
0
votes
3
replies
1.1k
views
Post-hoc filtering on the standard deviation in proportions
drimseq
rnaseqdtu
stager
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
Jack.Hearn
• 0
1
vote
1
reply
804
views
Calling a package specific function in a for loop
drimseq
swimming downstream
for loop
sapply
updated 5.6 years ago by
Martin Morgan
25k • written 5.6 years ago by
georgewwp
• 0
4
votes
3
replies
1.5k
views
DEXSeq and DRIMSeq on paired samples?
DRIMSeq
DEXSeq
updated 5.8 years ago by
Gosia Nowicka
▴ 90 • written 5.8 years ago by
zoe.ward
• 0
2
votes
9
replies
1.8k
views
stageR NA in getAdjustedPValues() (method=dtu)
drimseq
stageR
dtu
salmon rna seq
updated 6.0 years ago by
Koen Van den Berge
▴ 180 • written 6.0 years ago by
fiona.dick91
▴ 60
1
vote
1
reply
1.3k
views
DrimSeq: installation versions
drimseq
DTU
updated 6.9 years ago by
Martin Morgan
25k • written 6.9 years ago by
somseeprags
▴ 10
1
vote
2
replies
1.6k
views
Is it possible to get Isoform-level differential isoform usage form DRIMSeq?
DRIMSeq
splicing
differential isoform usage
updated 7.4 years ago by
Gosia Nowicka
▴ 90 • written 7.4 years ago by
kristoffer.vittingseerup
▴ 20
26 results • Page
1 of 1
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Comment: Trouble Installing DADA2 (warning: R new user)
by
shepherl
3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Answer: LRT test for different timepoints (one tissue types vs. many tissue types)
by
Michael Love
42k
No, this is a contrast of estimated coefficient (e.g. the Wald test).
Comment: Ranking the GSEA Results
by
Michael Love
42k
Got it. So then I'll take off DESeq2 as its mostly a downstream question. You may need to direct the fgsea developer to the thread. When yo…
Comment: Ranking the GSEA Results
by
V_Vibes
• 0
I have actually used the "fgsea" Bioconductor package which is used for GSEA. Thanks for pointing that out. I have edited that in the origi…
Comment: Ranking the GSEA Results
by
V_Vibes
• 0
The idea was inspired by people ranking the DEGs for preranked GSEA using their log2FC * (-log10 p-value). Also, the GSEA results I am gett…
Votes
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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