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gsva
•
reset
12
votes
10
replies
6.6k
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 5.3 years ago
rached
▴ 60
9
votes
7
replies
20k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea
gsva
piano
egsea
updated 5 months ago by
amin8w
▴ 10 • written 6.8 years ago by
sina.nassiri
▴ 130
8
votes
3
replies
2.5k
views
GSVA indifferent to 'abs.ranking'
GSVA
gsva
abs.ranking
updated 7.0 years ago by
Robert Castelo
★ 3.3k • written 7.0 years ago by
sina.nassiri
▴ 130
7
votes
11
replies
2.4k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
rocanja
▴ 60
6
votes
4
replies
1.8k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
3.2 years ago
hanyin.wang88
▴ 10
5
votes
16
replies
2.3k
views
GSVA package scores are opposite on mac and windows
GSVA
bug
gsva
bugs
updated 6.6 years ago by
Robert Castelo
★ 3.3k • written 6.6 years ago by
JasonL_Weirather
▴ 10
5
votes
9
replies
1.9k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
21 months ago
Yang Shi
▴ 10
5
votes
4
replies
3.1k
views
Differential expression on GSVA scores using LIMMA
limma
gsva
updated 5.1 years ago by
Robert Castelo
★ 3.3k • written 5.1 years ago by
rocanja
▴ 60
4
votes
2
replies
2.6k
views
GSVA: questions about the bootstrap p-value
gsva
updated 6.9 years ago by
Robert Castelo
★ 3.3k • written 6.9 years ago by
dionnezaal
▴ 30
4
votes
2
replies
1.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
Jonathan
▴ 10
3
votes
9
replies
8.8k
views
Does GSVA enrichment score comes negative?
GSVA
7.9 years ago • updated 7.0 years ago
pbachali
▴ 50
3
votes
4
replies
2.1k
views
Why Negative value from GSVA
GSVA
RNASeq
edgeR
22 months ago
Yang Shi
▴ 10
3
votes
2
replies
1.4k
views
Crash GSVA 1.24.0 with bootstrapping
GSVA
bug
updated 7.0 years ago by
Robert Castelo
★ 3.3k • written 7.0 years ago by
Sander Tan
▴ 20
2
votes
2
replies
3.5k
views
Error in running gsva function from GSVA package
gsva
updated 8.5 years ago by
Robert Castelo
★ 3.3k • written 8.5 years ago by
Momeneh Foroutan
▴ 10
2
votes
10
replies
3.7k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 3.9 years ago by
Robert Castelo
★ 3.3k • written 3.9 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 3.9 years ago by
Robert Castelo
★ 3.3k • written 3.9 years ago by
initialqy
• 0
2
votes
1
reply
2.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 3.8 years ago by
Robert Castelo
★ 3.3k • written 3.8 years ago by
igor
▴ 40
2
votes
3
replies
1.8k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 3.4 years ago by
Robert Castelo
★ 3.3k • written 3.4 years ago by
hsiowa2
▴ 20
2
votes
1
reply
3.3k
views
Dealing with the output of ssGSEA method from GSVA package
gsva
ssgsea
8.5 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
1.4k
views
Failed to install Biobase
GSVA
Biobase
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
johann.brisseau
• 0
2
votes
7
replies
1.8k
views
Issue with GSVA using dgCMatrix
GSVA
updated 8 weeks ago by
Moritz
▴ 10 • written 2.9 years ago by
resa
• 0
2
votes
5
replies
3.9k
views
GSVA error - incomplete instalation?
GSVA
ExpressionSet
8.5 years ago • updated 8.4 years ago
thrabe
• 0
2
votes
2
replies
842
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
2
replies
1.4k
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 6.1 years ago by
Robert Castelo
★ 3.3k • written 6.1 years ago by
CodeAway
▴ 70
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 5 months ago by
arina
• 0 • written 14 months ago by
Omer
• 0
2
votes
1
reply
1.2k
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA
tutorial
updated 5.6 years ago by
Robert Castelo
★ 3.3k • written 5.7 years ago by
owen.whitley
▴ 10
2
votes
5
replies
3.2k
views
Problem encountered when running GSVA for RNAseq
gsva
rnaseq
updated 9.5 years ago by
Robert Castelo
★ 3.3k • 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 5.2 years ago by
Pietro
▴ 40
1
vote
1
reply
1.2k
views
Cleaning GeneSets from GSEA
msigdb
GSEABase
GSVA
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 2.1 years ago by
forlani.luca
• 0
1
vote
11
replies
2.7k
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
1.4k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
5.8 years ago • updated 5.1 years ago
SB
• 0
1
vote
2
replies
515
views
GSVA error
GSVA
21 days ago • updated 20 days ago
Alex
• 0
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
★ 3.3k • written 5.8 years ago by
Shi-Xiang Wang
• 0
1
vote
3
replies
5.4k
views
GSVA and ssGSEA output differences
enrichment
GSVA
enrichplot
ssGSEA
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 2.1 years ago by
Davide
• 0
1
vote
4
replies
5.0k
views
GSVA on RNAseq data
gsva
rnaseq
updated 5.1 years ago by
Robert Castelo
★ 3.3k • written 5.1 years ago by
rocanja
▴ 60
1
vote
5
replies
1.5k
views
'combined score' calculation with singscore vs gsva
singscore
GSVA
18 months ago • updated 17 months ago
rocanja
▴ 60
1
vote
1
reply
1.7k
views
Method and kcdf arguments in gsva package
GSVA
updated 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
thkapell
▴ 10
1
vote
6
replies
493
views
GSVA on separate healthy and disease datasets
GSVA
updated 25 days ago by
James W. MacDonald
65k • written 26 days ago by
Lucy
▴ 60
1
vote
1
reply
627
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 5 months ago by
Robert Castelo
★ 3.3k • written 5 months ago by
snijesh
▴ 20
1
vote
2
replies
2.4k
views
GSVA for single sample
gsea
gsva
ssgsea
6.2 years ago
jaison75
▴ 20
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
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 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
Jenn
▴ 30
1
vote
2
replies
1.1k
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
2.7 years ago • updated 23 months ago
Guandong Shang
▴ 40
1
vote
2
replies
1.4k
views
Method to be used in gsva() function
GSVA
7.8 years ago
pbachali
▴ 50
0
votes
0
replies
70
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
6 days ago
Chris
• 0
0
votes
5
replies
5.2k
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
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Answer: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function?
by
Henrik Bengtsson
★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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