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rnaseqdtu
•
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2
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2
replies
903
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Inconsistent Dirichlet-multinominal coefficient and Beta-Binominal coefficient for a transcript in DTU analysis.
rnaseqDTU
DRIMSeq
2.5 years ago • updated 2.4 years ago
wangziwei0010
▴ 10
1
vote
5
replies
1.6k
views
Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
rnaseqDTU
2.7 years ago • updated 2.6 years ago
ksong
▴ 10
2
votes
7
replies
1.6k
views
Fold Change for rnaseq DTU
DEXSeq
rnaseqDTU
3.3 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
3.4 years ago
bioinformatic_trainee
▴ 10
0
votes
1
reply
744
views
Plotting results of rnaseqDTU
rnaseqDTU
updated 4.1 years ago by
Michael Love
43k • written 4.1 years ago by
rohitsatyam102
▴ 20
0
votes
1
reply
849
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu
RNASeq
DEXSeq
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
debatosh das
▴ 10
0
votes
2
replies
849
views
rnaseqDTU Workflow, Precision estimation error.
rnaseqDTU
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
dixit.anirudha
• 0
2
votes
2
replies
1.0k
views
Statistics for within-condition transcript abundance comparisons
rnaseqDTU
updated 5.3 years ago by
Michael Love
43k • written 5.3 years ago by
nicog
• 0
1
vote
3
replies
1.7k
views
Visualization for DE transcripts
rnaseqdtu
5.5 years ago
rbenel
▴ 40
1
vote
1
reply
1.6k
views
rnaseqDTU log2fold change DEXSeq
DEXSeq
DTU
salmon
rnaseqDTU
foldchange
updated 5.7 years ago by
Michael Love
43k • written 5.9 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
5.7 years ago
saddamhusain77
• 0
16
votes
25
replies
3.7k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.7 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
8
replies
1.5k
views
stageR following DEXSeq two-stage analysis
rnaseqdtu
5.9 years ago
rbenel
▴ 40
3
votes
9
replies
2.6k
views
Differential transcript expression (DTE) analysis
rnaseqDTU
dtu
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
rbenel
▴ 40
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 6.0 years ago by
Michael Love
43k • written 6.0 years ago by
Jack.Hearn
• 0
1
vote
5
replies
1.8k
views
Plotting Expression of Differential Transcripts plotDEXseq
DEXSeq
StageR
rnaseqDTU
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
rbenel
▴ 40
18 results • Page
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Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
Gordon Smyth
52k
Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
anna.cot.anna.cot
▴ 30
Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Tim Peters
▴ 200
Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
Gordon Smyth
52k
That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
James W. MacDonald
67k
Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…
Votes
Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
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