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rnaseqDTU
•
reset
16
votes
25
replies
3.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.1 years ago by
fiona.dick91
▴ 60
3
votes
9
replies
2.1k
views
Differential transcript expression (DTE) analysis
rnaseqDTU
dtu
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
rbenel
▴ 40
2
votes
2
replies
833
views
Statistics for within-condition transcript abundance comparisons
rnaseqDTU
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
nicog
• 0
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
2
votes
7
replies
1.2k
views
Fold Change for rnaseq DTU
DEXSeq
rnaseqDTU
2.7 years ago • updated 2.6 years ago
rbenel
▴ 40
2
votes
8
replies
1.2k
views
stageR following DEXSeq two-stage analysis
rnaseqdtu
5.2 years ago
rbenel
▴ 40
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
678
views
Inconsistent Dirichlet-multinominal coefficient and Beta-Binominal coefficient for a transcript in DTU analysis.
rnaseqDTU
DRIMSeq
21 months ago
wangziwei0010
▴ 10
1
vote
3
replies
1.2k
views
Visualization for DE transcripts
rnaseqdtu
4.8 years ago
rbenel
▴ 40
1
vote
1
reply
1.3k
views
rnaseqDTU log2fold change DEXSeq
DEXSeq
DTU
salmon
rnaseqDTU
foldchange
updated 5.0 years ago by
Michael Love
41k • written 5.3 years ago by
fiona.dick91
▴ 60
1
vote
5
replies
1.5k
views
Plotting Expression of Differential Transcripts plotDEXseq
DEXSeq
StageR
rnaseqDTU
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
rbenel
▴ 40
1
vote
5
replies
1.2k
views
Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
rnaseqDTU
2.1 years ago • updated 23 months ago
ksong
▴ 10
0
votes
1
reply
702
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu
RNASeq
DEXSeq
DESeq2
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
debatosh das
▴ 10
0
votes
1
reply
609
views
Plotting results of rnaseqDTU
rnaseqDTU
updated 3.5 years ago by
Michael Love
41k • written 3.5 years ago by
rohitsatyam102
▴ 20
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
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
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
0
votes
2
replies
697
views
rnaseqDTU Workflow, Precision estimation error.
rnaseqDTU
updated 3.9 years ago by
Michael Love
41k • written 3.9 years ago by
dixit.anirudha
• 0
18 results • Page
1 of 1
Recent ...
Replies
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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