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DRIMseq
•
reset
1
vote
1
reply
370
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
5 months ago
NiKo
▴ 10
0
votes
0
replies
379
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq
DRIMSeq
12 months ago
Luca
• 0
0
votes
3
replies
663
views
DRIMseq error for paired sample analysis
DRIMSeq
12 months ago
Luca
• 0
2
votes
2
replies
677
views
Inconsistent Dirichlet-multinominal coefficient and Beta-Binominal coefficient for a transcript in DTU analysis.
rnaseqDTU
DRIMSeq
21 months ago
wangziwei0010
▴ 10
0
votes
4
replies
1.4k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq
DRIMSeq
updated 23 months ago by
jeroen.gilis
▴ 90 • written 24 months ago by
phoebe1354
• 0
0
votes
5
replies
1.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
2.7 years ago
bioinformatic_trainee
▴ 10
3
votes
4
replies
1.1k
views
DRIMSeq: many NAs in results compared to DESeq2 ?
DESeq2
DRIMSeq
dtu
RNASeq
2.8 years ago
sbcn
▴ 80
0
votes
0
replies
861
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
3.1 years ago
jbono
▴ 10
0
votes
2
replies
985
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
3.1 years ago
Gaia
• 0
0
votes
5
replies
1.4k
views
Error using DRIMSeq with Salmon count data
DRIMSeq
tximport
txdb
Salmon
updated 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
Charlotte
• 0
1
vote
1
reply
794
views
Error in dmTest() from DRIMSeq package - tuQTL
DRIMSeq
tuQTL
updated 3.7 years ago by
Gosia Nowicka
▴ 90 • written 3.8 years ago by
iaradsouza1
• 0
0
votes
5
replies
1.1k
views
DRIMSeq with technical replicates
DRIMSeq
R
DTU
technical replicates
deseq2
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
poecile.pal
• 0
1
vote
1
reply
810
views
DEXSeq-DTU normalisation suggestion - scaledTPM vs dtuScaledTPM
tximport
DEXSeq-DTU
DRIMSeq
updated 3.9 years ago by
Michael Love
41k • written 3.9 years ago by
aleksandar.baburski.g
• 0
0
votes
0
replies
653
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq
DRIMSeq
3.9 years ago
alexis.weinreb
• 0
0
votes
11
replies
1.5k
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU
DRIMseq
DEXseq
rna-seq
5.1 years ago • updated 5.0 years ago
saddamhusain77
• 0
0
votes
1
reply
825
views
stageR with input from DRIMSeq
DRIMSeq
stageR
updated 5.1 years ago by
Koen Van den Berge
▴ 180 • written 5.1 years ago by
sdvie
• 0
1
vote
2
replies
1.4k
views
Normalized transcript/exon counts for network analysis
drimseq
dexseq
wgcna
sva
updated 5.2 years ago by
Gosia Nowicka
▴ 90 • written 5.2 years ago by
maya.kappil
▴ 30
0
votes
4
replies
1.4k
views
DRIMSeq continious variable in design matrix - Error during precision estimation
DRIMSeq
dmPrecision
updated 14 months ago by
Mary-Ellen
• 0 • written 5.2 years ago by
fiona.dick91
▴ 60
2
votes
4
replies
1.6k
views
stageR: Error in stageWiseAdjustment
stageR
rnaseqDTU
DRIMSeq
DEXSeq
5.2 years ago
d-joester
▴ 20
2
votes
2
replies
1.1k
views
rnaseqDTU DTU workflow - pots-hoc Filter
DTU
DRIMSeq
rnaseqDTU
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
fiona.dick91
▴ 60
0
votes
3
replies
1.0k
views
Post-hoc filtering on the standard deviation in proportions
drimseq
rnaseqdtu
stager
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
Jack.Hearn
• 0
1
vote
1
reply
761
views
Calling a package specific function in a for loop
drimseq
swimming downstream
for loop
sapply
updated 5.4 years ago by
Martin Morgan
25k • written 5.4 years ago by
georgewwp
• 0
4
votes
3
replies
1.4k
views
DEXSeq and DRIMSeq on paired samples?
DRIMSeq
DEXSeq
updated 5.6 years ago by
Gosia Nowicka
▴ 90 • written 5.6 years ago by
zoe.ward
• 0
2
votes
9
replies
1.7k
views
stageR NA in getAdjustedPValues() (method=dtu)
drimseq
stageR
dtu
salmon rna seq
updated 5.8 years ago by
Koen Van den Berge
▴ 180 • written 5.8 years ago by
fiona.dick91
▴ 60
1
vote
1
reply
1.3k
views
DrimSeq: installation versions
drimseq
DTU
updated 6.7 years ago by
Martin Morgan
25k • written 6.7 years ago by
somseeprags
▴ 10
1
vote
2
replies
1.5k
views
Is it possible to get Isoform-level differential isoform usage form DRIMSeq?
DRIMSeq
splicing
differential isoform usage
updated 7.2 years ago by
Gosia Nowicka
▴ 90 • written 7.2 years ago by
kristoffer.vittingseerup
▴ 20
26 results • Page
1 of 1
Recent ...
Replies
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Votes
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
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