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DRIMSeq
•
reset
1
vote
1
reply
613
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
12 months ago
NiKo
▴ 10
0
votes
0
replies
534
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq
DRIMSeq
19 months ago
Luca
• 0
0
votes
3
replies
896
views
DRIMseq error for paired sample analysis
DRIMSeq
19 months ago
Luca
• 0
2
votes
2
replies
870
views
Inconsistent Dirichlet-multinominal coefficient and Beta-Binominal coefficient for a transcript in DTU analysis.
rnaseqDTU
DRIMSeq
2.3 years ago
wangziwei0010
▴ 10
0
votes
4
replies
1.9k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq
DRIMSeq
updated 2.5 years ago by
jeroen.gilis
▴ 90 • written 2.5 years ago by
phoebe1354
• 0
0
votes
5
replies
1.5k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
3.2 years ago
bioinformatic_trainee
▴ 10
3
votes
4
replies
1.4k
views
DRIMSeq: many NAs in results compared to DESeq2 ?
DESeq2
DRIMSeq
dtu
RNASeq
3.3 years ago
sbcn
▴ 80
0
votes
0
replies
1.0k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
3.6 years ago
jbono
▴ 10
0
votes
2
replies
1.2k
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
3.6 years ago
Gaia
• 0
0
votes
5
replies
1.7k
views
Error using DRIMSeq with Salmon count data
DRIMSeq
tximport
txdb
Salmon
updated 4.2 years ago by
Michael Love
42k • written 4.3 years ago by
Charlotte
• 0
1
vote
1
reply
962
views
Error in dmTest() from DRIMSeq package - tuQTL
DRIMSeq
tuQTL
updated 4.3 years ago by
Gosia Nowicka
▴ 90 • written 4.3 years ago by
iaradsouza1
• 0
0
votes
5
replies
1.3k
views
DRIMSeq with technical replicates
DRIMSeq
R
DTU
technical replicates
deseq2
updated 4.3 years ago by
Kevin Blighe
★ 4.0k • written 4.3 years ago by
poecile.pal
• 0
1
vote
1
reply
955
views
DEXSeq-DTU normalisation suggestion - scaledTPM vs dtuScaledTPM
tximport
DEXSeq-DTU
DRIMSeq
updated 4.4 years ago by
Michael Love
42k • written 4.4 years ago by
aleksandar.baburski.g
• 0
0
votes
0
replies
784
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq
DRIMSeq
4.5 years ago
alexis.weinreb
• 0
0
votes
11
replies
1.8k
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU
DRIMseq
DEXseq
rna-seq
5.6 years ago
saddamhusain77
• 0
0
votes
1
reply
976
views
stageR with input from DRIMSeq
DRIMSeq
stageR
updated 5.7 years ago by
Koen Van den Berge
▴ 180 • written 5.7 years ago by
sdvie
• 0
1
vote
2
replies
1.7k
views
Normalized transcript/exon counts for network analysis
drimseq
dexseq
wgcna
sva
updated 5.7 years ago by
Gosia Nowicka
▴ 90 • written 5.7 years ago by
maya.kappil
▴ 30
0
votes
4
replies
1.7k
views
DRIMSeq continious variable in design matrix - Error during precision estimation
DRIMSeq
dmPrecision
updated 21 months ago by
Mary-Ellen
• 0 • written 5.8 years ago by
fiona.dick91
▴ 60
2
votes
4
replies
1.9k
views
stageR: Error in stageWiseAdjustment
stageR
rnaseqDTU
DRIMSeq
DEXSeq
5.8 years ago
d-joester
▴ 20
2
votes
2
replies
1.3k
views
rnaseqDTU DTU workflow - pots-hoc Filter
DTU
DRIMSeq
rnaseqDTU
updated 5.8 years ago by
Michael Love
42k • written 5.8 years ago by
fiona.dick91
▴ 60
0
votes
3
replies
1.2k
views
Post-hoc filtering on the standard deviation in proportions
drimseq
rnaseqdtu
stager
updated 5.9 years ago by
Michael Love
42k • written 5.9 years ago by
Jack.Hearn
• 0
1
vote
1
reply
910
views
Calling a package specific function in a for loop
drimseq
swimming downstream
for loop
sapply
updated 5.9 years ago by
Martin Morgan
25k • written 5.9 years ago by
georgewwp
• 0
4
votes
3
replies
1.6k
views
DEXSeq and DRIMSeq on paired samples?
DRIMSeq
DEXSeq
updated 6.1 years ago by
Gosia Nowicka
▴ 90 • written 6.1 years ago by
zoe.ward
• 0
2
votes
9
replies
2.0k
views
stageR NA in getAdjustedPValues() (method=dtu)
drimseq
stageR
dtu
salmon rna seq
updated 6.3 years ago by
Koen Van den Berge
▴ 180 • written 6.3 years ago by
fiona.dick91
▴ 60
1
vote
1
reply
1.4k
views
DrimSeq: installation versions
drimseq
DTU
updated 7.3 years ago by
Martin Morgan
25k • written 7.3 years ago by
somseeprags
▴ 10
1
vote
2
replies
1.7k
views
Is it possible to get Isoform-level differential isoform usage form DRIMSeq?
DRIMSeq
splicing
differential isoform usage
updated 7.8 years ago by
Gosia Nowicka
▴ 90 • written 7.8 years ago by
kristoffer.vittingseerup
▴ 20
26 results • Page
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Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
Adam Marstrand
• 0
Thank you!
Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
Adam Marstrand
• 0
Hi Gordon, Thanks for the answer! This makes a lot of sense. Your suggested pipeline (separate processing of datasets -> gene set analyses…
Comment: How many of my genes from my gene list are in each KEGG pathway?
by
josephasmith1310
• 0
> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…
Comment: EuroBioC2024 abstract submission is open!
by
Esperan
• 0
Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
by
Gordon Smyth
51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Votes
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
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