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rnaseqDTU
•
reset
16
votes
25
replies
3.6k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.6 years ago by
fiona.dick91
▴ 60
2
votes
2
replies
873
views
Inconsistent Dirichlet-multinominal coefficient and Beta-Binominal coefficient for a transcript in DTU analysis.
rnaseqDTU
DRIMSeq
2.4 years ago
wangziwei0010
▴ 10
1
vote
5
replies
1.5k
views
Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
rnaseqDTU
2.6 years ago • updated 2.5 years ago
ksong
▴ 10
2
votes
7
replies
1.6k
views
Fold Change for rnaseq DTU
DEXSeq
rnaseqDTU
3.2 years ago
rbenel
▴ 40
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
3.3 years ago
bioinformatic_trainee
▴ 10
0
votes
1
reply
718
views
Plotting results of rnaseqDTU
rnaseqDTU
updated 4.0 years ago by
Michael Love
42k • written 4.0 years ago by
rohitsatyam102
▴ 20
0
votes
1
reply
828
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu
RNASeq
DEXSeq
DESeq2
updated 4.4 years ago by
Michael Love
42k • written 4.4 years ago by
debatosh das
▴ 10
0
votes
2
replies
829
views
rnaseqDTU Workflow, Precision estimation error.
rnaseqDTU
updated 4.5 years ago by
Michael Love
42k • written 4.5 years ago by
dixit.anirudha
• 0
2
votes
2
replies
973
views
Statistics for within-condition transcript abundance comparisons
rnaseqDTU
updated 5.2 years ago by
Michael Love
42k • written 5.2 years ago by
nicog
• 0
1
vote
3
replies
1.6k
views
Visualization for DE transcripts
rnaseqdtu
5.4 years ago
rbenel
▴ 40
1
vote
1
reply
1.5k
views
rnaseqDTU log2fold change DEXSeq
DEXSeq
DTU
salmon
rnaseqDTU
foldchange
updated 5.6 years ago by
Michael Love
42k • written 5.8 years ago by
fiona.dick91
▴ 60
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
2
votes
4
replies
1.9k
views
stageR: Error in stageWiseAdjustment
stageR
rnaseqDTU
DRIMSeq
DEXSeq
5.8 years ago
d-joester
▴ 20
2
votes
8
replies
1.5k
views
stageR following DEXSeq two-stage analysis
rnaseqdtu
5.8 years ago
rbenel
▴ 40
3
votes
9
replies
2.5k
views
Differential transcript expression (DTE) analysis
rnaseqDTU
dtu
updated 5.8 years ago by
Michael Love
42k • written 5.8 years ago by
rbenel
▴ 40
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
5
replies
1.8k
views
Plotting Expression of Differential Transcripts plotDEXseq
DEXSeq
StageR
rnaseqDTU
updated 6.1 years ago by
Michael Love
42k • written 6.1 years ago by
rbenel
▴ 40
18 results • Page
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Answer: Is it possible to parallelise saveHDF5SummarizedExperiment
by
Hervé Pagès
16k
Hi Stefano, Unfortunately HDF5 doesn't support concurrent writing so parallelising is not an option. A few things that maybe could help: …
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
James W. MacDonald
67k
It's a simple two-liner in [getsrc.sh][1] ``` awk -F'\t' 'BEGIN {OFS=FS} {if($3 != $11 && $11 != "-") $3 = $11; print $0}' gene_info > tmp…
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
Guido Hooiveld
★ 4.1k
Thanks for changing this! Just to confirm I understood it correctly: the `Symbol` will (still) be used, and will be replaced by `Symbol fro…
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
James W. MacDonald
67k
OK, there are 157 MT genes in maybe 6 species for which the symbols are not correct, and I added code to swap the 'Symbol from nomenclature…
Comment: Tximport with RSEM error
by
Michael Love
42k
Would you post a new issue with example code and maybe what the files look like?
Votes
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
Answer: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
A: GOseq analysis with only upregulated or downregulated genes
A: GOseq analysis with only upregulated or downregulated genes
Answer: Properly constructing a hypergeometric test
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