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drimseq
•
reset
0
votes
0
replies
78
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq
DRIMSeq
8 weeks ago
Luca
• 0
0
votes
3
replies
186
views
DRIMseq error for paired sample analysis
DRIMSeq
8 weeks ago • updated 7 weeks ago
Luca
• 0
2
votes
2
replies
356
views
Inconsistent Dirichlet-multinominal coefficient and Beta-Binominal coefficient for a transcript in DTU analysis.
rnaseqDTU
DRIMSeq
10 months ago
wangziwei0010
▴ 10
0
votes
4
replies
710
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq
DRIMSeq
updated 12 months ago by
jeroen.gilis
▴ 90 • written 13 months ago by
phoebe1354
• 0
0
votes
5
replies
669
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
21 months ago
bioinformatic_trainee
▴ 10
3
votes
4
replies
664
views
DRIMSeq: many NAs in results compared to DESeq2 ?
DESeq2
DRIMSeq
dtu
RNASeq
22 months ago
sbcn
▴ 80
0
votes
0
replies
490
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
2.2 years ago
jbono
▴ 10
0
votes
2
replies
569
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
2.2 years ago
Gaia
• 0
0
votes
5
replies
1.0k
views
Error using DRIMSeq with Salmon count data
DRIMSeq
tximport
txdb
Salmon
updated 2.8 years ago by
Michael Love
40k • written 2.8 years ago by
Charlotte
• 0
1
vote
1
reply
508
views
Error in dmTest() from DRIMSeq package - tuQTL
DRIMSeq
tuQTL
updated 2.8 years ago by
Gosia Nowicka
▴ 90 • written 2.9 years ago by
iaradsouza1
• 0
0
votes
5
replies
663
views
DRIMSeq with technical replicates
DRIMSeq
R
DTU
technical replicates
deseq2
updated 2.9 years ago by
Kevin Blighe
3.8k • written 2.9 years ago by
poecile.pal
• 0
1
vote
1
reply
529
views
DEXSeq-DTU normalisation suggestion - scaledTPM vs dtuScaledTPM
tximport
DEXSeq-DTU
DRIMSeq
updated 2.9 years ago by
Michael Love
40k • written 2.9 years ago by
aleksandar.baburski.g
• 0
0
votes
0
replies
409
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq
DRIMSeq
3.0 years ago
alexis.weinreb
• 0
0
votes
11
replies
1.1k
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU
DRIMseq
DEXseq
rna-seq
4.2 years ago • updated 4.1 years ago
saddamhusain77
• 0
0
votes
1
reply
598
views
stageR with input from DRIMSeq
DRIMSeq
stageR
updated 4.2 years ago by
Koen Van den Berge
▴ 180 • written 4.2 years ago by
sdvie
• 0
1
vote
2
replies
914
views
Normalized transcript/exon counts for network analysis
drimseq
dexseq
wgcna
sva
updated 4.3 years ago by
Gosia Nowicka
▴ 90 • written 4.3 years ago by
maya.kappil
▴ 20
0
votes
4
replies
988
views
DRIMSeq continious variable in design matrix - Error during precision estimation
DRIMSeq
dmPrecision
updated 3 months ago by
Mary-Ellen
• 0 • written 4.3 years ago by
fiona.dick91
▴ 10
2
votes
4
replies
1.2k
views
stageR: Error in stageWiseAdjustment
stageR
rnaseqDTU
DRIMSeq
DEXSeq
4.3 years ago
d-joester
▴ 20
2
votes
2
replies
812
views
rnaseqDTU DTU workflow - pots-hoc Filter
DTU
DRIMSeq
rnaseqDTU
updated 4.4 years ago by
Michael Love
40k • written 4.4 years ago by
fiona.dick91
▴ 10
0
votes
3
replies
769
views
Post-hoc filtering on the standard deviation in proportions
drimseq
rnaseqdtu
stager
updated 4.5 years ago by
Michael Love
40k • written 4.5 years ago by
Jack.Hearn
• 0
1
vote
1
reply
518
views
Calling a package specific function in a for loop
drimseq
swimming downstream
for loop
sapply
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
georgewwp
• 0
4
votes
3
replies
975
views
DEXSeq and DRIMSeq on paired samples?
DRIMSeq
DEXSeq
updated 4.7 years ago by
Gosia Nowicka
▴ 90 • written 4.7 years ago by
zoe.ward
• 0
2
votes
9
replies
1.2k
views
stageR NA in getAdjustedPValues() (method=dtu)
drimseq
stageR
dtu
salmon rna seq
updated 4.9 years ago by
Koen Van den Berge
▴ 180 • written 4.9 years ago by
fiona.dick91
▴ 10
1
vote
1
reply
1.1k
views
DrimSeq: installation versions
drimseq
DTU
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
somseeprags
▴ 10
1
vote
2
replies
1.2k
views
Is it possible to get Isoform-level differential isoform usage form DRIMSeq?
DRIMSeq
splicing
differential isoform usage
updated 6.3 years ago by
Gosia Nowicka
▴ 90 • written 6.3 years ago by
kristoffer.vittingseerup
▴ 20
25 results • Page
1 of 1
Recent ...
Replies
Comment: Question on constructing design matrix and defining contrasts for analysis
by
mohammedtoufiq91
▴ 10
@gordonsmyth thank you, yes, please find the targets frame below. Basically, I want to create a design matrix and binarize by 0 and 1 to be…
Comment: WGCNA: many over and under-expressed features in modules of a signed network
by
andres.firrincieli
▴ 50
answered in Biostars: https://www.biostars.org/p/9564943/
Comment: Multitasking and Rbwa
by
Jean-Philippe Fortin
• 0
Indeed, one can pass additional arguments to the `bwa_aln` function in `Rbwa`: bwa_aln(type="single", index_prefix=index_pr…
Comment: biomaRt error: database disk image is malformed
by
Emile
• 0
UNBORKING the bioMaRt cache `biomaRt::biomartCacheClear()` also fixes the troubles with PANTHER.db installation which have also something t…
Answer: Proteomics data with NA values
by
Laurent Gatto
1.6k
- First, you need to assess how many missing values you have. - I would recommend not to impute your data by 0 (or any arbitrary small …
Votes
Answer: Question on constructing design matrix and defining contrasts for analysis
WGCNA: many over and under-expressed features in modules of a signed network
Comment: WGCNA: many over and under-expressed features in modules of a signed network
Answer: DESeq2 or edgeR for Presence and Absence of Proteins
Answer: Normalized counts from LRT or Wald test?
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