Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
gsva
•
reset
1
vote
2
replies
311
views
Can limma be used with module eigengenes instead of genes?
limma
WGCNA
GSVA
written 3 months ago by
A.Barden
▴ 10
1
vote
2
replies
1.3k
views
GSVA 1.52.2 (new API) nb of workers?
parallelize
workers
GSVA
written 17 months ago by
johanna.galvis
• 0
1
vote
1
reply
1.9k
views
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 8 months ago by
ATpoint
★ 5.0k • written 8 months ago by
amien.vp
• 0
5
votes
5
replies
1.8k
views
Unused arguments error without used arguments in GSVA?
GSVA
updated 7 months ago by
michaelarringtony
• 0 • written 9 months ago by
1sunmic2
• 0
1
vote
2
replies
1.1k
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
11 months ago
georgii.vdovin
• 0
1
vote
5
replies
1.2k
views
Identifying potentially associated gene set to drug response using GSVA
drug
RNASeq
GSVA
written 12 months ago by
Kent
• 0
5
votes
4
replies
2.7k
views
GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment
GSVA
ssGSEA
updated 12 months ago by
Tyler Sagendorf
▴ 10 • written 13 months ago by
Bob
▴ 30
0
votes
1
reply
1.6k
views
Job:
Research software engineer at UPF Barcelona
JobPosting
Devel
GSVA
Software
written 3.0 years ago by
Robert Castelo
★ 3.4k
0
votes
1
reply
1.1k
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea
GSVA
gsea
updated 15 months ago by
Axel Klenk
★ 1.1k • written 15 months ago by
Bioinformagician
• 0
1
vote
4
replies
2.5k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA
GSVAdata
RNAseq
16 months ago • updated 15 months ago
Lucy
▴ 60
1
vote
2
replies
940
views
Interpretation of GSVA with absRanking=TRUE
GSVA
17 months ago
gad.abraham
• 0
0
votes
3
replies
2.0k
views
GSVA function
DESeq2
GSVA
ssGSEA
updated 17 months ago by
Robert Castelo
★ 3.4k • written 17 months ago by
michelafrancesconi8
• 0
4
votes
5
replies
1.9k
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
18 months ago
Chris
▴ 20
0
votes
1
reply
1.2k
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
written 18 months ago by
Chris
▴ 20
1
vote
2
replies
6.0k
views
GSVA error
GSVA
19 months ago
Alex
• 0
1
vote
6
replies
1.5k
views
GSVA on separate healthy and disease datasets
GSVA
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Lucy
▴ 60
4
votes
4
replies
4.8k
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 13 months ago by
tifaGis
• 0 • written 23 months ago by
snijesh
▴ 200
0
votes
1
reply
929
views
GSVA exceeds 1
GSVA
updated 2.2 years ago by
Robert Castelo
★ 3.4k • written 2.2 years ago by
Heba
• 0
4
votes
2
replies
3.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 2.4 years ago by
Gordon Smyth
53k • written 2.4 years ago by
Jonathan
▴ 10
2
votes
0
replies
2.5k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
2.6 years ago
Tadeoye
▴ 20
0
votes
2
replies
1.5k
views
GSVA with and without absolute scaling method
GSVA
2.6 years ago
arashdeep singh
• 0
2
votes
4
replies
2.7k
views
Failed to install Biobase
GSVA
Biobase
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
johann.brisseau
• 0
3
votes
6
replies
3.5k
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
escape
UCell
GSVA
updated 23 months ago by
arina
▴ 10 • written 2.7 years ago by
Omer
• 0
0
votes
3
replies
1.5k
views
GSVA: Error loading interactive web app
igsva
GSVA
updated 2.7 years ago by
Robert Castelo
★ 3.4k • written 2.8 years ago by
sharvari gujja
▴ 40
0
votes
3
replies
2.7k
views
GSVA results interpretation
GSVA
updated 2.8 years ago by
Robert Castelo
★ 3.4k • written 2.8 years ago by
munta.jihad
• 0
0
votes
0
replies
1.4k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
2.9 years ago
Zhijie
• 0
1
vote
5
replies
2.8k
views
'combined score' calculation with singscore vs gsva
singscore
GSVA
3.0 years ago
rocanja
▴ 60
5
votes
9
replies
3.0k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
3.3 years ago
Yang Shi
▴ 10
3
votes
4
replies
3.6k
views
Why Negative value from GSVA
GSVA
RNASeq
edgeR
3.4 years ago
Yang Shi
▴ 10
0
votes
3
replies
3.8k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA
GSVA
updated 3.0 years ago by
rocanja
▴ 60 • written 3.4 years ago by
João
• 0
1
vote
2
replies
1.8k
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
4.2 years ago • updated 3.4 years ago
Guandong Shang
▴ 40
2
votes
2
replies
2.5k
views
How to run GSVA with partially NA genes
GSVA
3.5 years ago
blakebowen
• 0
1
vote
3
replies
10k
views
GSVA and ssGSEA output differences
enrichment
GSVA
enrichplot
ssGSEA
updated 3.6 years ago by
Robert Castelo
★ 3.4k • written 3.6 years ago by
Davide
• 0
1
vote
1
reply
2.5k
views
Cleaning GeneSets from GSEA
msigdb
GSEABase
GSVA
updated 3.6 years ago by
Robert Castelo
★ 3.4k • written 3.6 years ago by
forlani.luca
• 0
0
votes
1
reply
1.2k
views
Running PLAGE gets killed
GSVA
SingleCellData
updated 3.7 years ago by
Robert Castelo
★ 3.4k • written 3.7 years ago by
Amna
• 0
0
votes
1
reply
2.1k
views
GSVA: for a pathway, can enrichment scores of all samples be negative?
GSVAdata
GSVA
updated 3.7 years ago by
Robert Castelo
★ 3.4k • written 3.7 years ago by
random
• 0
0
votes
1
reply
2.1k
views
GSVA package normalization on gene-length ?
GSVA
updated 3.9 years ago by
Robert Castelo
★ 3.4k • written 3.9 years ago by
xanthexu
• 0
1
vote
11
replies
3.6k
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 4.3 years ago by
soudayo
▴ 10 • written 5.2 years ago by
yaoxucpu
• 0
2
votes
2
replies
3.1k
views
Questions regard to GSVA and Limma
limma
GSVA
4.4 years ago
Chenxi
• 0
2
votes
2
replies
1.3k
views
Turn of GSVA filtering for method ssGSEA
GSVA
4.4 years ago
k.vitting.seerup
▴ 120
2
votes
7
replies
4.7k
views
Issue with GSVA using dgCMatrix
GSVA
updated 20 months ago by
Moritz
▴ 10 • written 4.4 years ago by
resa
• 0
0
votes
1
reply
4.7k
views
GSVA Problem
GSVA
updated 4.5 years ago by
Robert Castelo
★ 3.4k • written 4.5 years ago by
tywzlzl2011
• 0
6
votes
4
replies
2.5k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
4.8 years ago • updated 4.7 years ago
hanyin.wang88
▴ 10
0
votes
8
replies
9.1k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 3.1 years ago by
Robert Castelo
★ 3.4k • written 4.8 years ago by
Siyuan
• 0
2
votes
3
replies
3.0k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 4.9 years ago by
Robert Castelo
★ 3.4k • written 4.9 years ago by
hsiowa2
▴ 20
0
votes
3
replies
2.3k
views
GSVA on gene sets with 2 genes
GSVA
gene sets
RNA-seq
updated 5.0 years ago by
Robert Castelo
★ 3.4k • written 5.1 years ago by
Endre Sebestyén
▴ 70
0
votes
1
reply
1.8k
views
Extract GSVA gene rank matrix
gsva
updated 5.3 years ago by
Robert Castelo
★ 3.4k • written 5.3 years ago by
dylan
• 0
2
votes
1
reply
3.4k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 5.3 years ago by
Robert Castelo
★ 3.4k • written 5.3 years ago by
igor
▴ 50
2
votes
2
replies
2.6k
views
Using GSVA All the pathway score are same
GSVA
scRNA-seq data
updated 5.4 years ago by
Robert Castelo
★ 3.4k • written 5.4 years ago by
initialqy
• 0
2
votes
10
replies
5.3k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 5.4 years ago by
Robert Castelo
★ 3.4k • written 5.4 years ago by
hsiowa2
▴ 20
99 results • Page
1 of 2
Recent ...
Replies
Answer: Post translational modifications and phosphoproteomics in limpa?
by
Gordon Smyth
53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
by
Matthew Thornton
▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated
by
RalphSavage99
• 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2
by
shepherl
4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed.
by
Kevin Blighe
★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Awards
• All
Popular Question
to
Hervé Pagès
16k
Popular Question
to
shepherl
4.2k
Scholar
to
James W. MacDonald
68k
Popular Question
to
Daniel Cameron
▴ 40
Popular Question
to
Peter Hickey
▴ 760
Locations
• All
The city by the bay,
14 minutes ago
WEHI, Melbourne, Australia,
52 minutes ago
WEHI, Melbourne, Australia,
1 hour ago
United States,
1 hour ago
Pittsburgh, United States,
2 hours ago
Traffic: 1181 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6