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Showing :
drimseq
•
reset
1
vote
1
reply
655
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
13 months ago
NiKo
▴ 10
0
votes
0
replies
557
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq
DRIMSeq
20 months ago
Luca
• 0
0
votes
3
replies
933
views
DRIMseq error for paired sample analysis
DRIMSeq
20 months ago
Luca
• 0
2
votes
2
replies
908
views
Inconsistent Dirichlet-multinominal coefficient and Beta-Binominal coefficient for a transcript in DTU analysis.
rnaseqDTU
DRIMSeq
2.5 years ago
wangziwei0010
▴ 10
0
votes
4
replies
2.0k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq
DRIMSeq
updated 2.6 years ago by
jeroen.gilis
▴ 90 • written 2.6 years ago by
phoebe1354
• 0
0
votes
5
replies
1.6k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
3.4 years ago
bioinformatic_trainee
▴ 10
3
votes
4
replies
1.4k
views
DRIMSeq: many NAs in results compared to DESeq2 ?
DESeq2
DRIMSeq
dtu
RNASeq
3.4 years ago
sbcn
▴ 80
0
votes
0
replies
1.1k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
3.7 years ago
jbono
▴ 10
0
votes
2
replies
1.2k
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
3.8 years ago
Gaia
• 0
0
votes
5
replies
1.7k
views
Error using DRIMSeq with Salmon count data
DRIMSeq
tximport
txdb
Salmon
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
Charlotte
• 0
1
vote
1
reply
994
views
Error in dmTest() from DRIMSeq package - tuQTL
DRIMSeq
tuQTL
updated 4.4 years ago by
Gosia Nowicka
▴ 90 • written 4.4 years ago by
iaradsouza1
• 0
0
votes
5
replies
1.4k
views
DRIMSeq with technical replicates
DRIMSeq
R
DTU
technical replicates
deseq2
updated 4.4 years ago by
Kevin Blighe
★ 4.0k • written 4.4 years ago by
poecile.pal
• 0
1
vote
1
reply
982
views
DEXSeq-DTU normalisation suggestion - scaledTPM vs dtuScaledTPM
tximport
DEXSeq-DTU
DRIMSeq
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
aleksandar.baburski.g
• 0
0
votes
0
replies
830
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq
DRIMSeq
4.6 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
5.7 years ago
saddamhusain77
• 0
0
votes
1
reply
1.0k
views
stageR with input from DRIMSeq
DRIMSeq
stageR
updated 5.8 years ago by
Koen Van den Berge
▴ 180 • written 5.8 years ago by
sdvie
• 0
1
vote
2
replies
1.7k
views
Normalized transcript/exon counts for network analysis
drimseq
dexseq
wgcna
sva
updated 5.8 years ago by
Gosia Nowicka
▴ 90 • written 5.8 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 22 months ago by
Mary-Ellen
• 0 • written 5.9 years ago by
fiona.dick91
▴ 60
2
votes
4
replies
1.9k
views
stageR: Error in stageWiseAdjustment
stageR
rnaseqDTU
DRIMSeq
DEXSeq
5.9 years ago
d-joester
▴ 20
2
votes
2
replies
1.3k
views
rnaseqDTU DTU workflow - pots-hoc Filter
DTU
DRIMSeq
rnaseqDTU
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
fiona.dick91
▴ 60
0
votes
3
replies
1.3k
views
Post-hoc filtering on the standard deviation in proportions
drimseq
rnaseqdtu
stager
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
Jack.Hearn
• 0
1
vote
1
reply
929
views
Calling a package specific function in a for loop
drimseq
swimming downstream
for loop
sapply
updated 6.1 years ago by
Martin Morgan
25k • written 6.1 years ago by
georgewwp
• 0
4
votes
3
replies
1.7k
views
DEXSeq and DRIMSeq on paired samples?
DRIMSeq
DEXSeq
updated 6.2 years ago by
Gosia Nowicka
▴ 90 • written 6.2 years ago by
zoe.ward
• 0
2
votes
9
replies
2.1k
views
stageR NA in getAdjustedPValues() (method=dtu)
drimseq
stageR
dtu
salmon rna seq
updated 6.4 years ago by
Koen Van den Berge
▴ 180 • written 6.4 years ago by
fiona.dick91
▴ 60
1
vote
1
reply
1.4k
views
DrimSeq: installation versions
drimseq
DTU
updated 7.4 years ago by
Martin Morgan
25k • written 7.4 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 7.9 years ago by
Gosia Nowicka
▴ 90 • written 7.9 years ago by
kristoffer.vittingseerup
▴ 20
26 results • Page
1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma
by
Ali Barry
▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
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Ali Barry
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gabriel.hoffman
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