Showing : 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 ▴ 10 • written 6.8 years ago by ▴ 130
8
votes
3
replies
2.5k
views
GSVA indifferent to 'abs.ranking'
GSVA gsva abs.ranking
updated 7.0 years ago by ★ 3.3k • written 7.0 years ago by ▴ 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 ★ 3.3k • written 4.0 years ago by ▴ 60
6
votes
4
replies
1.8k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
3.3 years ago hanyin.wang88 ▴ 10
5
votes
4
replies
3.1k
views
Differential expression on GSVA scores using LIMMA
limma gsva
updated 5.1 years ago by ★ 3.3k • written 5.1 years ago by ▴ 60
5
votes
9
replies
1.9k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
22 months ago • updated 21 months ago Yang Shi ▴ 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 ★ 3.3k • written 6.6 years ago by ▴ 10
4
votes
2
replies
1.3k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 10 months ago by 50k • written 10 months ago by ▴ 10
4
votes
2
replies
2.6k
views
GSVA: questions about the bootstrap p-value
gsva
updated 6.9 years ago by ★ 3.3k • written 6.9 years ago by ▴ 30
4
votes
5
replies
314
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
11 days ago • updated 2 days ago Chris ▴ 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 ★ 3.3k • written 7.0 years ago by ▴ 20
2
votes
2
replies
848
views
Turn of GSVA filtering for method ssGSEA
GSVA
2.9 years ago k.vitting.seerup ▴ 120
2
votes
0
replies
1.1k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
13 months ago Tadeoye ▴ 20
2
votes
5
replies
4.0k
views
GSVA error - incomplete instalation?
GSVA ExpressionSet
8.5 years ago thrabe • 0
2
votes
2
replies
1.4k
views
How to run GSVA with partially NA genes
GSVA
24 months ago blakebowen • 0
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 ★ 3.3k • written 3.9 years ago by ▴ 20
2
votes
1
reply
2.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 3.8 years ago by ★ 3.3k • written 3.8 years ago by ▴ 50
2
votes
6
replies
1.7k
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
escape UCell GSVA
updated 5 months ago by • 0 • written 15 months ago by • 0
2
votes
2
replies
3.6k
views
Error in running gsva function from GSVA package
gsva
updated 8.5 years ago by ★ 3.3k • written 8.5 years ago by ▴ 10
2
votes
1
reply
1.2k
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA tutorial
updated 5.7 years ago by ★ 3.3k • written 5.7 years ago by ▴ 10
2
votes
3
replies
1.9k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 3.4 years ago by ★ 3.3k • written 3.4 years ago by ▴ 20
2
votes
5
replies
3.2k
views
Problem encountered when running GSVA for RNAseq
gsva rnaseq
updated 9.6 years ago by ★ 3.3k • written 9.6 years ago by • 0
2
votes
4
replies
2.5k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 3.4 years ago by • 0 • written 5.2 years ago by ▴ 40
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
1.8k
views
Input genes for GSVA
gsva gene expression matrix
updated 6.1 years ago by ★ 3.3k • written 6.1 years ago by ▴ 70
2
votes
2
replies
2.0k
views
Questions regard to GSVA and Limma
limma GSVA
2.9 years ago Chenxi • 0
2
votes
4
replies
1.4k
views
Failed to install Biobase
GSVA Biobase
updated 13 months ago by 65k • written 13 months ago by • 0
2
votes
7
replies
1.8k
views
Issue with GSVA using dgCMatrix
GSVA
updated 10 weeks ago by ▴ 10 • written 2.9 years ago by • 0
2
votes
2
replies
1.9k
views
Using GSVA All the pathway score are same
GSVA scRNA-seq data
updated 3.9 years ago by ★ 3.3k • written 3.9 years ago by • 0
1
vote
2
replies
1.4k
views
Method to be used in gsva() function
GSVA
7.8 years ago pbachali ▴ 50
1
vote
0
replies
1.6k
views
Pre-processing of RNA sequencing data for GSVA
rnaseq rna-seq preprocessing gsva
7.8 years ago t.kuilman ▴ 170
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 ▴ 10 • written 3.7 years ago by • 0
1
vote
2
replies
701
views
GSVA error
GSVA
4 weeks ago Alex • 0
1
vote
1
reply
1.2k
views
Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 2.1 years ago by ★ 3.3k • written 2.1 years ago by • 0
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
1
reply
694
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea GSVA biotype proteincoding msigdb
updated 5 months ago by ★ 3.3k • written 5 months ago by ▴ 20
1
vote
5
replies
1.6k
views
'combined score' calculation with singscore vs gsva
singscore GSVA
18 months ago rocanja ▴ 60
1
vote
3
replies
5.6k
views
GSVA and ssGSEA output differences
enrichment GSVA enrichplot ssGSEA
updated 2.1 years ago by ★ 3.3k • written 2.1 years ago by • 0
1
vote
2
replies
2.4k
views
GSVA for single sample
gsea gsva ssgsea
6.3 years ago jaison75 ▴ 20
1
vote
1
reply
1.5k
views
GSVA with NanoString nCounter data
GSVA Nanostring
5.8 years ago • updated 5.1 years ago SB • 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 ★ 3.3k • written 5.8 years ago by • 0
1
vote
6
replies
522
views
GSVA on separate healthy and disease datasets
GSVA
updated 5 weeks ago by 65k • written 5 weeks ago by ▴ 60
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
5.4 years ago krassowski.michal ▴ 40
1
vote
4
replies
5.0k
views
GSVA on RNAseq data
gsva rnaseq
updated 5.1 years ago by ★ 3.3k • written 5.1 years ago by ▴ 60
1
vote
1
reply
1.7k
views
Method and kcdf arguments in gsva package
GSVA
updated 4.1 years ago by ★ 3.3k • written 4.1 years ago by ▴ 10
1
vote
12
replies
2.4k
views
GSVA (running group samples separately)
GSVA
updated 4.0 years ago by ★ 3.3k • written 4.0 years ago by ▴ 30
0
votes
0
replies
94
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
18 days ago Chris ▴ 10
50 results • Page 1 of 1
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Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
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If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
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Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
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