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gsva
•
reset
12
votes
10
replies
9.7k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva
gene set variation analysis
normalization
transformation
rna-seq
7.8 years ago • updated 7.0 years ago
rached
▴ 60
9
votes
7
replies
23k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea
gsva
piano
egsea
updated 2.1 years ago by
amin8w
▴ 10 • written 8.5 years ago by
sina.nassiri
▴ 130
8
votes
3
replies
3.4k
views
GSVA indifferent to 'abs.ranking'
GSVA
gsva
abs.ranking
updated 8.7 years ago by
Robert Castelo
★ 3.4k • written 8.7 years ago by
sina.nassiri
▴ 130
7
votes
11
replies
4.4k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 5.7 years ago by
Robert Castelo
★ 3.4k • written 5.7 years ago by
rocanja
▴ 60
6
votes
4
replies
2.6k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
4.9 years ago
hanyin.wang88
▴ 10
5
votes
9
replies
3.1k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
3.5 years ago
Yang Shi
▴ 10
5
votes
4
replies
3.3k
views
GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment
GSVA
ssGSEA
updated 14 months ago by
Tyler Sagendorf
▴ 10 • written 15 months ago by
Bob
▴ 30
5
votes
5
replies
2.4k
views
Unused arguments error without used arguments in GSVA?
GSVA
updated 9 months ago by
michaelarringtony
• 0 • written 11 months ago by
1sunmic2
• 0
5
votes
4
replies
4.8k
views
Differential expression on GSVA scores using LIMMA
limma
gsva
updated 6.8 years ago by
Robert Castelo
★ 3.4k • written 6.8 years ago by
rocanja
▴ 60
5
votes
16
replies
3.5k
views
GSVA package scores are opposite on mac and windows
GSVA
bug
gsva
bugs
updated 8.3 years ago by
Robert Castelo
★ 3.4k • written 8.3 years ago by
JasonL_Weirather
▴ 10
4
votes
2
replies
3.4k
views
GSVA: questions about the bootstrap p-value
gsva
updated 8.6 years ago by
Robert Castelo
★ 3.4k • written 8.6 years ago by
dionnezaal
▴ 30
4
votes
2
replies
3.6k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
Jonathan
▴ 10
4
votes
4
replies
5.5k
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 15 months ago by
tifaGis
• 0 • written 2.1 years ago by
snijesh
▴ 200
4
votes
5
replies
2.1k
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
20 months ago
Chris
▴ 20
3
votes
2
replies
1.9k
views
Crash GSVA 1.24.0 with bootstrapping
GSVA
bug
updated 8.7 years ago by
Robert Castelo
★ 3.4k • written 8.7 years ago by
Sander Tan
▴ 20
3
votes
6
replies
3.8k
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
escape
UCell
GSVA
updated 2.1 years ago by
arina
▴ 10 • written 2.9 years ago by
Omer
• 0
3
votes
9
replies
12k
views
Does GSVA enrichment score comes negative?
GSVA
9.5 years ago • updated 8.7 years ago
pbachali
▴ 50
3
votes
4
replies
3.8k
views
Why Negative value from GSVA
GSVA
RNASeq
edgeR
3.5 years ago
Yang Shi
▴ 10
2
votes
3
replies
3.2k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 5.0 years ago by
Robert Castelo
★ 3.4k • written 5.1 years ago by
hsiowa2
▴ 20
2
votes
1
reply
1.6k
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA
tutorial
updated 7.3 years ago by
Robert Castelo
★ 3.4k • written 7.3 years ago by
owen.whitley
▴ 10
2
votes
2
replies
2.6k
views
How to run GSVA with partially NA genes
GSVA
3.6 years ago
blakebowen
• 0
2
votes
4
replies
3.8k
views
Are singscore scores comparable between gene sets?
singscore
GSVA
GSEA
subtypes
geneset
updated 5.0 years ago by
Dharmesh D Bhuva
• 0 • written 6.8 years ago by
Pietro
▴ 40
2
votes
0
replies
2.7k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
2.8 years ago
Tadeoye
▴ 20
2
votes
2
replies
1.4k
views
Turn of GSVA filtering for method ssGSEA
GSVA
4.5 years ago
k.vitting.seerup
▴ 120
2
votes
7
replies
5.1k
views
Issue with GSVA using dgCMatrix
GSVA
updated 22 months ago by
Moritz
▴ 10 • written 4.6 years ago by
resa
• 0
2
votes
4
replies
2.9k
views
Failed to install Biobase
GSVA
Biobase
updated 2.8 years ago by
James W. MacDonald
68k • written 2.8 years ago by
johann.brisseau
• 0
2
votes
2
replies
3.2k
views
Questions regard to GSVA and Limma
limma
GSVA
4.5 years ago
Chenxi
• 0
2
votes
5
replies
4.4k
views
Problem encountered when running GSVA for RNAseq
gsva
rnaseq
updated 11.2 years ago by
Robert Castelo
★ 3.4k • written 11.2 years ago by
polly0806
• 0
2
votes
2
replies
2.8k
views
Input genes for GSVA
gsva
gene expression matrix
updated 7.7 years ago by
Robert Castelo
★ 3.4k • written 7.8 years ago by
CodeAway
▴ 70
2
votes
2
replies
6.7k
views
Error in running gsva function from GSVA package
gsva
updated 10.2 years ago by
Robert Castelo
★ 3.4k • written 10.2 years ago by
Momeneh Foroutan
▴ 10
2
votes
1
reply
4.4k
views
Dealing with the output of ssGSEA method from GSVA package
gsva
ssgsea
10.2 years ago
Momeneh Foroutan
▴ 10
2
votes
5
replies
6.4k
views
GSVA error - incomplete instalation?
GSVA
ExpressionSet
10.2 years ago • updated 10.1 years ago
thrabe
• 0
2
votes
1
reply
3.6k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 5.5 years ago by
Robert Castelo
★ 3.4k • written 5.5 years ago by
igor
▴ 50
2
votes
2
replies
2.7k
views
Using GSVA All the pathway score are same
GSVA
scRNA-seq data
updated 5.6 years ago by
Robert Castelo
★ 3.4k • written 5.6 years ago by
initialqy
• 0
2
votes
10
replies
5.5k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 5.6 years ago by
Robert Castelo
★ 3.4k • written 5.6 years ago by
hsiowa2
▴ 20
1
vote
4
replies
2.9k
views
Meaning of zero for ssGESA value calculated by GSVA package
gsva
updated 7.5 years ago by
Robert Castelo
★ 3.4k • written 7.5 years ago by
Shi-Xiang Wang
• 0
1
vote
2
replies
2.1k
views
Method to be used in gsva() function
GSVA
9.5 years ago
pbachali
▴ 50
1
vote
0
replies
2.0k
views
Pre-processing of RNA sequencing data for GSVA
rnaseq
rna-seq
preprocessing
gsva
9.4 years ago
t.kuilman
▴ 170
1
vote
2
replies
3.4k
views
GSVA for single sample
gsea
gsva
ssgsea
7.9 years ago
jaison75
▴ 20
1
vote
1
reply
2.1k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
7.5 years ago • updated 6.8 years ago
SB
• 0
1
vote
1
reply
1.9k
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
7.0 years ago
krassowski.michal
▴ 40
1
vote
6
replies
7.8k
views
GSVA on RNAseq data
gsva
rnaseq
updated 11 months ago by
Robert Castelo
★ 3.4k • written 6.8 years ago by
rocanja
▴ 60
1
vote
1
reply
3.2k
views
Method and kcdf arguments in gsva package
GSVA
updated 5.7 years ago by
Robert Castelo
★ 3.4k • written 5.7 years ago by
thkapell
▴ 10
1
vote
12
replies
3.9k
views
GSVA (running group samples separately)
GSVA
updated 5.7 years ago by
Robert Castelo
★ 3.4k • written 5.7 years ago by
Jenn
▴ 30
1
vote
11
replies
3.8k
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 4.5 years ago by
soudayo
▴ 10 • written 5.4 years ago by
yaoxucpu
• 0
1
vote
2
replies
6.4k
views
GSVA error
GSVA
21 months ago
Alex
• 0
1
vote
2
replies
1.1k
views
Interpretation of GSVA with absRanking=TRUE
GSVA
19 months ago
gad.abraham
• 0
1
vote
1
reply
2.6k
views
Cleaning GeneSets from GSEA
msigdb
GSEABase
GSVA
updated 3.8 years ago by
Robert Castelo
★ 3.4k • written 3.8 years ago by
forlani.luca
• 0
1
vote
2
replies
1.9k
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
4.4 years ago • updated 3.6 years ago
Guandong Shang
▴ 40
1
vote
2
replies
1.2k
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
13 months ago
georgii.vdovin
• 0
99 results • Page
1 of 2
Recent ...
Replies
Comment: Joining different datasets and analyzing using the group-specific condition effe
by
James W. MacDonald
68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Comment: Joining different datasets and analyzing using the group-specific condition effe
by
jason.chai
• 0
@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…
Comment: Clarification on counting in Rsubread (featureCounts)
by
Luca
• 0
Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …
Comment: Clarification on counting in Rsubread (featureCounts)
by
Gordon Smyth
53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts)
by
Frances Turner
▴ 20
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Votes
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
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