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gsva
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655
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GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct" and "unused arguments (exprsData = as.matrix(rna_seq_sub), gset.idx…
GSVA
updated 21 days ago by
ATpoint
★ 4.7k • written 21 days ago by
amien.vp
• 0
5
votes
4
replies
976
views
Unused arguments error without used arguments in GSVA?
GSVA
updated 6 weeks ago by
Axel Klenk
★ 1.1k • written 7 weeks ago by
1sunmic2
• 0
1
vote
2
replies
657
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
3 months ago
georgii.vdovin
• 0
1
vote
5
replies
697
views
Identifying potentially associated gene set to drug response using GSVA
drug
RNASeq
GSVA
written 4 months ago by
Kent
• 0
1
vote
4
replies
1.5k
views
GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment
GSVA
ssGSEA
updated 4 months ago by
Tyler Sagendorf
▴ 10 • written 5 months ago by
Bob
▴ 10
0
votes
1
reply
695
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea
GSVA
gsea
updated 7 months ago by
Axel Klenk
★ 1.1k • written 7 months ago by
Bioinformagician
• 0
1
vote
4
replies
1.8k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA
GSVAdata
RNAseq
8 months ago
Lucy
▴ 60
1
vote
1
reply
655
views
GSVA 1.52.2 (new API) nb of workers?
parallelize
workers
GSVA
updated 9 months ago by
Axel Klenk
★ 1.1k • written 9 months ago by
johanna.galvis
• 0
1
vote
2
replies
642
views
Interpretation of GSVA with absRanking=TRUE
GSVA
9 months ago
gad.abraham
• 0
0
votes
3
replies
1.4k
views
GSVA function
DESeq2
GSVA
ssGSEA
updated 9 months ago by
Robert Castelo
★ 3.4k • written 10 months ago by
michelafrancesconi8
• 0
4
votes
5
replies
1.4k
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
10 months ago
Chris
▴ 20
0
votes
0
replies
439
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
10 months ago
Chris
▴ 20
1
vote
2
replies
4.8k
views
GSVA error
GSVA
11 months ago
Alex
• 0
1
vote
6
replies
1.1k
views
GSVA on separate healthy and disease datasets
GSVA
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Lucy
▴ 60
4
votes
4
replies
3.3k
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 5 months ago by
tifaGis
• 0 • written 15 months ago by
snijesh
▴ 200
0
votes
1
reply
1.3k
views
Job:
Research software engineer at UPF Barcelona
JobPosting
Devel
GSVA
Software
written 2.3 years ago by
Robert Castelo
★ 3.4k
1
vote
6
replies
6.8k
views
GSVA on RNAseq data
gsva
rnaseq
updated 5 weeks ago by
Robert Castelo
★ 3.4k • written 6.0 years ago by
rocanja
▴ 60
17 results • Page
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Comment: DiffBind custom normalization factor
by
Abbie
• 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
by
Michael Love
43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
A: use tximport's countsFromAbundance when using DESeq2
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