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Isoforms
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2
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989
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Confounding DE results with DESeq2
isoforms
DESeq2
2.7 years ago
arfranco
▴ 130
1
vote
9
replies
2.3k
views
Difference between gene-level test and transcript-level test with RATs (Relative Abundance of Transcrits)
RATs
RNA-Seq
Isoforms
DTU
expression
updated 5.4 years ago by
fruce_ki
▴ 20 • written 5.4 years ago by
UserAnonyme
• 0
0
votes
3
replies
1.7k
views
Downstream analysis for Salmon output: IsoformSwitchAnalyzeR or TSIS?
isoforms
diffrential expression
noncoding rna
TSIS
isoformswitchanalyzeR
6.6 years ago
rbenel
▴ 40
0
votes
0
replies
1.1k
views
Metadata sheet for DEXSeq analysis
dexseq
differential isoform usage
isoforms
summarizeoverlaps
granges
6.7 years ago
A
▴ 40
0
votes
0
replies
1.7k
views
cummeRbund heatmap for specific isoforms (not genes)
cummerbund
heatmap
isoforms
transcript_id
7.7 years ago
domenico.somma
• 0
5
votes
18
replies
3.7k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq
bitseq
cuffdiff
Differential exon usage
isoforms
9.6 years ago • updated 9.5 years ago
elle
▴ 10
5
votes
3
replies
2.7k
views
edgeR: annotation and isoform analysis alternatives
edgeR
ruvseq
rnaseq
isoforms
9.6 years ago
sergio.espeso-gil
• 0
1
vote
2
replies
1.5k
views
DEXSeq transcripts per condition
DEXSeq
transcripts
isoforms
updated 9.6 years ago by
Alejandro Reyes
★ 1.9k • written 9.6 years ago by
peter_venhuizen
• 0
8 results • Page
1 of 1
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Replies
Comment: Feature Counts - potential bug with outfile.jcounts
by
Gordon Smyth
52k
I agree that the current behavior is not fully satisfactory and, indeed, it has prevented me from using the junction read counts from featu…
Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
• 0
Hi Gordon, Sorry, I didn't see the added response to your original answer. I think that would be a great idea; a novel junction to annot…
Comment: Cannot install GO.db and org.Hs.eg.db
by
Gabriel
• 0
The downloaded source packages are in 'C:Users\gabri\AppData\Local\Temp\RtmpailNer\downloaded_packages' Installation paths not writeable, …
Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
• 0
Hi Gordon, Thank you for pointing out that FeatureCounts detects junction reads de novo. It is not in the manual, and maybe could be. Give…
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
by
Michael Love
43k
I've seen in some papers ~1 TPM for saying something in mouse/human etc. was "minimally expressed". For an average length gene, 10 count…
Votes
Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
A: Relations used in GO.db GOBPANCESTOR
Relations used in GO.db GOBPANCESTOR
Answer: RSubread output significantly different from bash Subread output
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