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drimseq
•
reset
1
vote
1
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368
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
5 months ago
NiKo
▴ 10
0
votes
3
replies
663
views
DRIMseq error for paired sample analysis
DRIMSeq
12 months ago
Luca
• 0
0
votes
0
replies
377
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq
DRIMSeq
12 months ago
Luca
• 0
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
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
860
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
809
views
DEXSeq-DTU normalisation suggestion - scaledTPM vs dtuScaledTPM
tximport
DEXSeq-DTU
DRIMSeq
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
aleksandar.baburski.g
• 0
0
votes
0
replies
652
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
824
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
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
760
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: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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