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Isoforms
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2
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777
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Confounding DE results with DESeq2
isoforms
DESeq2
2.1 years ago
arfranco
▴ 130
1
vote
9
replies
1.9k
views
Difference between gene-level test and transcript-level test with RATs (Relative Abundance of Transcrits)
RATs
RNA-Seq
Isoforms
DTU
expression
updated 4.8 years ago by
fruce_ki
▴ 20 • written 4.8 years ago by
UserAnonyme
• 0
0
votes
3
replies
1.4k
views
Downstream analysis for Salmon output: IsoformSwitchAnalyzeR or TSIS?
isoforms
diffrential expression
noncoding rna
TSIS
isoformswitchanalyzeR
5.9 years ago
rbenel
▴ 40
0
votes
0
replies
956
views
Metadata sheet for DEXSeq analysis
dexseq
differential isoform usage
isoforms
summarizeoverlaps
granges
6.1 years ago
A
▴ 40
0
votes
0
replies
1.5k
views
cummeRbund heatmap for specific isoforms (not genes)
cummerbund
heatmap
isoforms
transcript_id
7.1 years ago
domenico.somma
• 0
5
votes
18
replies
3.1k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq
bitseq
cuffdiff
Differential exon usage
isoforms
8.9 years ago • updated 8.8 years ago
elle
▴ 10
5
votes
3
replies
2.4k
views
edgeR: annotation and isoform analysis alternatives
edgeR
ruvseq
rnaseq
isoforms
8.9 years ago
sergio.espeso-gil
• 0
1
vote
2
replies
1.4k
views
DEXSeq transcripts per condition
DEXSeq
transcripts
isoforms
updated 8.9 years ago by
Alejandro Reyes
★ 1.9k • written 9.0 years ago by
peter_venhuizen
• 0
8 results • Page
1 of 1
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Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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