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Isoforms
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983
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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
1.6k
views
Downstream analysis for Salmon output: IsoformSwitchAnalyzeR or TSIS?
isoforms
diffrential expression
noncoding rna
TSIS
isoformswitchanalyzeR
6.5 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
1.6k
views
cummeRbund heatmap for specific isoforms (not genes)
cummerbund
heatmap
isoforms
transcript_id
7.7 years ago
domenico.somma
• 0
5
votes
18
replies
3.6k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq
bitseq
cuffdiff
Differential exon usage
isoforms
9.5 years ago • updated 9.4 years ago
elle
▴ 10
5
votes
3
replies
2.7k
views
edgeR: annotation and isoform analysis alternatives
edgeR
ruvseq
rnaseq
isoforms
9.5 years ago
sergio.espeso-gil
• 0
1
vote
2
replies
1.5k
views
DEXSeq transcripts per condition
DEXSeq
transcripts
isoforms
updated 9.5 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
Answer: Deseq2 res Function
by
Michael Love
43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Answer: ANOVA like approach of edgeR
by
Gordon Smyth
51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data
by
Gordon Smyth
51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix?
by
NB
• 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix?
by
James W. MacDonald
67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Votes
Comment: Is it recommended to analyze different tissues together when using edgeR
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
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