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Isoforms
•
reset
2
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2
replies
1.1k
views
Confounding DE results with DESeq2
isoforms
DESeq2
3.1 years ago
arfranco
▴ 130
1
vote
9
replies
2.6k
views
Difference between gene-level test and transcript-level test with RATs (Relative Abundance of Transcrits)
RATs
RNA-Seq
Isoforms
DTU
expression
updated 5.8 years ago by
fruce_ki
▴ 20 • written 5.8 years ago by
UserAnonyme
• 0
0
votes
3
replies
1.9k
views
Downstream analysis for Salmon output: IsoformSwitchAnalyzeR or TSIS?
isoforms
diffrential expression
noncoding rna
TSIS
isoformswitchanalyzeR
6.9 years ago
rbenel
▴ 40
0
votes
0
replies
1.2k
views
Metadata sheet for DEXSeq analysis
dexseq
differential isoform usage
isoforms
summarizeoverlaps
granges
7.1 years ago
A
▴ 60
0
votes
0
replies
1.7k
views
cummeRbund heatmap for specific isoforms (not genes)
cummerbund
heatmap
isoforms
transcript_id
8.1 years ago
domenico.somma
• 0
5
votes
18
replies
4.0k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq
bitseq
cuffdiff
Differential exon usage
isoforms
9.9 years ago • updated 9.8 years ago
elle
▴ 10
5
votes
3
replies
2.9k
views
edgeR: annotation and isoform analysis alternatives
edgeR
ruvseq
rnaseq
isoforms
9.9 years ago
sergio.espeso-gil
• 0
1
vote
2
replies
1.6k
views
DEXSeq transcripts per condition
DEXSeq
transcripts
isoforms
updated 9.9 years ago by
Alejandro Reyes
★ 1.9k • written 10.0 years ago by
peter_venhuizen
• 0
8 results • Page
1 of 1
Recent ...
Replies
Comment: CluserProfiler message "No gene can be mapped"
by
Carolina
• 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2
by
JKim
• 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE
by
James W. MacDonald
68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation
by
sergisayolspuig
▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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