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GSVA
•
reset
12
votes
10
replies
6.4k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva
gene set variation analysis
normalization
transformation
rna-seq
6.1 years ago • updated 5.2 years ago
rached
▴ 60
9
votes
7
replies
20k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea
gsva
piano
egsea
updated 4 months ago by
amin8w
▴ 10 • written 6.7 years ago by
sina.nassiri
▴ 130
8
votes
3
replies
2.4k
views
GSVA indifferent to 'abs.ranking'
GSVA
gsva
abs.ranking
updated 7.0 years ago by
Robert Castelo
★ 3.2k • written 7.0 years ago by
sina.nassiri
▴ 130
7
votes
11
replies
2.3k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 4.0 years ago by
Robert Castelo
★ 3.2k • written 4.0 years ago by
rocanja
▴ 60
6
votes
4
replies
1.7k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
3.2 years ago
hanyin.wang88
▴ 10
5
votes
4
replies
3.0k
views
Differential expression on GSVA scores using LIMMA
limma
gsva
updated 5.0 years ago by
Robert Castelo
★ 3.2k • written 5.1 years ago by
rocanja
▴ 60
5
votes
9
replies
1.8k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
21 months ago
Yang Shi
▴ 10
5
votes
16
replies
2.2k
views
GSVA package scores are opposite on mac and windows
GSVA
bug
gsva
bugs
updated 6.5 years ago by
Robert Castelo
★ 3.2k • written 6.5 years ago by
JasonL_Weirather
▴ 10
4
votes
2
replies
2.5k
views
GSVA: questions about the bootstrap p-value
gsva
updated 6.8 years ago by
Robert Castelo
★ 3.2k • written 6.8 years ago by
dionnezaal
▴ 30
3
votes
4
replies
2.0k
views
Why Negative value from GSVA
GSVA
RNASeq
edgeR
21 months ago
Yang Shi
▴ 10
3
votes
9
replies
8.7k
views
Does GSVA enrichment score comes negative?
GSVA
7.8 years ago • updated 7.0 years ago
pbachali
▴ 50
3
votes
2
replies
1.4k
views
Crash GSVA 1.24.0 with bootstrapping
GSVA
bug
updated 7.0 years ago by
Robert Castelo
★ 3.2k • written 7.0 years ago by
Sander Tan
▴ 20
3
votes
2
replies
1.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
Jonathan
▴ 10
2
votes
6
replies
1.6k
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
escape
UCell
GSVA
updated 4 months ago by
arina
• 0 • written 14 months ago by
Omer
• 0
2
votes
10
replies
3.6k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 3.8 years ago by
Robert Castelo
★ 3.2k • written 3.8 years ago by
hsiowa2
▴ 20
2
votes
2
replies
1.8k
views
Using GSVA All the pathway score are same
GSVA
scRNA-seq data
updated 3.8 years ago by
Robert Castelo
★ 3.2k • written 3.8 years ago by
initialqy
• 0
2
votes
1
reply
2.0k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 3.8 years ago by
Robert Castelo
★ 3.2k • written 3.8 years ago by
igor
▴ 40
2
votes
2
replies
3.5k
views
Error in running gsva function from GSVA package
gsva
updated 8.4 years ago by
Robert Castelo
★ 3.2k • written 8.4 years ago by
Momeneh Foroutan
▴ 10
2
votes
3
replies
1.8k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 3.3 years ago by
Robert Castelo
★ 3.2k • written 3.3 years ago by
hsiowa2
▴ 20
2
votes
1
reply
3.3k
views
Dealing with the output of ssGSEA method from GSVA package
gsva
ssgsea
8.4 years ago
Momeneh Foroutan
▴ 10
2
votes
2
replies
2.0k
views
Questions regard to GSVA and Limma
limma
GSVA
2.8 years ago
Chenxi
• 0
2
votes
4
replies
1.3k
views
Failed to install Biobase
GSVA
Biobase
updated 12 months ago by
James W. MacDonald
65k • written 12 months ago by
johann.brisseau
• 0
2
votes
7
replies
1.7k
views
Issue with GSVA using dgCMatrix
GSVA
updated 6 weeks ago by
Moritz
▴ 10 • written 2.8 years ago by
resa
• 0
2
votes
2
replies
826
views
Turn of GSVA filtering for method ssGSEA
GSVA
2.8 years ago
k.vitting.seerup
▴ 120
2
votes
0
replies
1.1k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
12 months ago
Tadeoye
▴ 20
2
votes
5
replies
3.9k
views
GSVA error - incomplete instalation?
GSVA
ExpressionSet
8.4 years ago
thrabe
• 0
2
votes
2
replies
1.3k
views
How to run GSVA with partially NA genes
GSVA
23 months ago
blakebowen
• 0
2
votes
2
replies
1.8k
views
Input genes for GSVA
gsva
gene expression matrix
updated 6.0 years ago by
Robert Castelo
★ 3.2k • written 6.0 years ago by
CodeAway
▴ 70
2
votes
1
reply
1.1k
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA
tutorial
updated 5.6 years ago by
Robert Castelo
★ 3.2k • written 5.6 years ago by
owen.whitley
▴ 10
2
votes
5
replies
3.1k
views
Problem encountered when running GSVA for RNAseq
gsva
rnaseq
updated 9.5 years ago by
Robert Castelo
★ 3.2k • written 9.5 years ago by
polly0806
• 0
2
votes
4
replies
2.4k
views
Are singscore scores comparable between gene sets?
singscore
GSVA
GSEA
subtypes
geneset
updated 3.3 years ago by
Dharmesh D Bhuva
• 0 • written 5.1 years ago by
Pietro
▴ 40
1
vote
2
replies
1.1k
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
2.6 years ago • updated 22 months ago
Guandong Shang
▴ 40
1
vote
4
replies
4.9k
views
GSVA on RNAseq data
gsva
rnaseq
updated 5.0 years ago by
Robert Castelo
★ 3.2k • written 5.0 years ago by
rocanja
▴ 60
1
vote
1
reply
1.2k
views
Cleaning GeneSets from GSEA
msigdb
GSEABase
GSVA
updated 2.1 years ago by
Robert Castelo
★ 3.2k • written 2.1 years ago by
forlani.luca
• 0
1
vote
1
reply
1.4k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
5.8 years ago • updated 5.0 years ago
SB
• 0
1
vote
2
replies
1.4k
views
Method to be used in gsva() function
GSVA
7.8 years ago
pbachali
▴ 50
1
vote
4
replies
2.0k
views
Meaning of zero for ssGESA value calculated by GSVA package
gsva
updated 5.8 years ago by
Robert Castelo
★ 3.2k • written 5.8 years ago by
Shi-Xiang Wang
• 0
1
vote
6
replies
432
views
GSVA on separate healthy and disease datasets
GSVA
updated 9 days ago by
James W. MacDonald
65k • written 10 days ago by
Lucy
▴ 60
1
vote
3
replies
5.3k
views
GSVA and ssGSEA output differences
enrichment
GSVA
enrichplot
ssGSEA
updated 2.0 years ago by
Robert Castelo
★ 3.2k • written 2.0 years ago by
Davide
• 0
1
vote
1
reply
1.7k
views
Method and kcdf arguments in gsva package
GSVA
updated 4.0 years ago by
Robert Castelo
★ 3.2k • written 4.0 years ago by
thkapell
▴ 10
1
vote
1
reply
1.3k
views
PLAGE method fails in GSVA if an overlap between gene sets and genes in expressions is less than two
gsva
plage
differential expression
gene set enrichment
5.3 years ago
krassowski.michal
▴ 40
1
vote
5
replies
1.5k
views
'combined score' calculation with singscore vs gsva
singscore
GSVA
17 months ago
rocanja
▴ 60
1
vote
2
replies
2.3k
views
GSVA for single sample
gsea
gsva
ssgsea
6.2 years ago
jaison75
▴ 20
1
vote
0
replies
1.6k
views
Pre-processing of RNA sequencing data for GSVA
rnaseq
rna-seq
preprocessing
gsva
7.7 years ago
t.kuilman
▴ 170
1
vote
12
replies
2.4k
views
GSVA (running group samples separately)
GSVA
updated 3.9 years ago by
Robert Castelo
★ 3.2k • written 3.9 years ago by
Jenn
▴ 30
1
vote
2
replies
235
views
GSVA error
GSVA
5 days ago • updated 4 days ago
Alex
• 0
1
vote
11
replies
2.6k
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 2.8 years ago by
soudayo
▴ 10 • written 3.7 years ago by
yaoxucpu
• 0
1
vote
1
reply
565
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 4 months ago by
Robert Castelo
★ 3.2k • written 4 months ago by
snijesh
▴ 20
0
votes
1
reply
932
views
GSVA lots of positive values, is this expected behavior?
gsva
updated 5.0 years ago by
Robert Castelo
★ 3.2k • written 5.0 years ago by
owen.whitley
▴ 10
0
votes
5
replies
5.1k
views
Convert gene expression matrix to ExpressionSet
GSVA
GSVA
updated 12.5 years ago by
Martin Morgan
25k • written 12.5 years ago by
Wendy Qiao
▴ 360
50 results • Page
1 of 1
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Comment: Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
by
christianhilton64
• 0
I'm less familiar with the specifics of GSVA, but I'm curious about the overall goal of this analysis. Could you provide a high-level summa…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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