Showing : gsva • reset
12
votes
10
replies
7.9k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva gene set variation analysis normalization transformation rna-seq
6.8 years ago • updated 6.0 years ago rached ▴ 60
9
votes
7
replies
21k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea gsva piano egsea
updated 13 months ago by ▴ 10 • written 7.5 years ago by ▴ 130
8
votes
3
replies
2.9k
views
GSVA indifferent to 'abs.ranking'
GSVA gsva abs.ranking
updated 7.7 years ago by ★ 3.4k • written 7.7 years ago by ▴ 130
7
votes
11
replies
3.2k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.7 years ago by ★ 3.4k • written 4.7 years ago by ▴ 60
6
votes
4
replies
2.1k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
3.9 years ago hanyin.wang88 ▴ 10
5
votes
9
replies
2.4k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.5 years ago Yang Shi ▴ 10
5
votes
16
replies
2.8k
views
GSVA package scores are opposite on mac and windows
GSVA bug gsva bugs
updated 7.3 years ago by ★ 3.4k • written 7.3 years ago by ▴ 10
5
votes
4
replies
3.9k
views
Differential expression on GSVA scores using LIMMA
limma gsva
updated 5.8 years ago by ★ 3.4k • written 5.8 years ago by ▴ 60
4
votes
5
replies
1.2k
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
8 months ago Chris ▴ 20
4
votes
4
replies
2.5k
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea GSVA biotype proteincoding msigdb
updated 3 months ago by • 0 • written 13 months ago by ▴ 200
4
votes
2
replies
2.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 18 months ago by 52k • written 18 months ago by ▴ 10
4
votes
2
replies
3.0k
views
GSVA: questions about the bootstrap p-value
gsva
updated 7.6 years ago by ★ 3.4k • written 7.6 years ago by ▴ 30
3
votes
2
replies
1.6k
views
Crash GSVA 1.24.0 with bootstrapping
GSVA bug
updated 7.7 years ago by ★ 3.4k • written 7.7 years ago by ▴ 20
3
votes
9
replies
10k
views
Does GSVA enrichment score comes negative?
GSVA
8.6 years ago • updated 7.7 years ago pbachali ▴ 50
3
votes
4
replies
2.8k
views
Why Negative value from GSVA
GSVA RNASeq edgeR
2.5 years ago Yang Shi ▴ 10
2
votes
5
replies
5.0k
views
GSVA error - incomplete instalation?
GSVA ExpressionSet
9.2 years ago • updated 9.1 years ago thrabe • 0
2
votes
10
replies
4.5k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 4.6 years ago by ★ 3.4k • written 4.6 years ago by ▴ 20
2
votes
6
replies
2.5k
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
escape UCell GSVA
updated 13 months ago by • 0 • written 23 months ago by • 0
2
votes
1
reply
2.7k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 4.5 years ago by ★ 3.4k • written 4.5 years ago by ▴ 50
2
votes
2
replies
2.2k
views
Input genes for GSVA
gsva gene expression matrix
updated 6.8 years ago by ★ 3.4k • written 6.8 years ago by ▴ 70
2
votes
2
replies
2.0k
views
How to run GSVA with partially NA genes
GSVA
2.7 years ago blakebowen • 0
2
votes
0
replies
1.9k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
21 months ago Tadeoye ▴ 20
2
votes
1
reply
1.3k
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA tutorial
updated 6.3 years ago by ★ 3.4k • written 6.4 years ago by ▴ 10
2
votes
2
replies
1.1k
views
Turn of GSVA filtering for method ssGSEA
GSVA
3.6 years ago k.vitting.seerup ▴ 120
2
votes
7
replies
3.2k
views
Issue with GSVA using dgCMatrix
GSVA
updated 10 months ago by ▴ 10 • written 3.6 years ago by • 0
2
votes
4
replies
2.1k
views
Failed to install Biobase
GSVA Biobase
updated 22 months ago by 67k • written 22 months ago by • 0
2
votes
2
replies
2.5k
views
Questions regard to GSVA and Limma
limma GSVA
3.6 years ago Chenxi • 0
2
votes
3
replies
2.4k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 4.1 years ago by ★ 3.4k • written 4.1 years ago by ▴ 20
2
votes
5
replies
3.7k
views
Problem encountered when running GSVA for RNAseq
gsva rnaseq
updated 10.2 years ago by ★ 3.4k • written 10.2 years ago by • 0
2
votes
4
replies
3.0k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 4.0 years ago by • 0 • written 5.9 years ago by ▴ 40
2
votes
2
replies
2.3k
views
Using GSVA All the pathway score are same
GSVA scRNA-seq data
updated 4.6 years ago by ★ 3.4k • written 4.6 years ago by • 0
2
votes
2
replies
5.0k
views
Error in running gsva function from GSVA package
gsva
updated 9.2 years ago by ★ 3.4k • written 9.2 years ago by ▴ 10
2
votes
1
reply
3.7k
views
Dealing with the output of ssGSEA method from GSVA package
gsva ssgsea
9.2 years ago Momeneh Foroutan ▴ 10
1
vote
3
replies
8.1k
views
GSVA and ssGSEA output differences
enrichment GSVA enrichplot ssGSEA
updated 2.8 years ago by ★ 3.4k • written 2.8 years ago by • 0
1
vote
2
replies
1.6k
views
Method to be used in gsva() function
GSVA
8.5 years ago pbachali ▴ 50
1
vote
0
replies
1.8k
views
Pre-processing of RNA sequencing data for GSVA
rnaseq rna-seq preprocessing gsva
8.4 years ago t.kuilman ▴ 170
1
vote
2
replies
2.8k
views
GSVA for single sample
gsea gsva ssgsea
6.9 years ago jaison75 ▴ 20
1
vote
1
reply
1.7k
views
GSVA with NanoString nCounter data
GSVA Nanostring
6.5 years ago • updated 5.8 years ago SB • 0
1
vote
4
replies
2.3k
views
Meaning of zero for ssGESA value calculated by GSVA package
gsva
updated 6.5 years ago by ★ 3.4k • written 6.5 years ago by • 0
1
vote
1
reply
1.5k
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
6.0 years ago krassowski.michal ▴ 40
1
vote
4
replies
6.2k
views
GSVA on RNAseq data
gsva rnaseq
updated 5.8 years ago by ★ 3.4k • written 5.8 years ago by ▴ 60
1
vote
1
reply
2.3k
views
Method and kcdf arguments in gsva package
GSVA
updated 4.7 years ago by ★ 3.4k • written 4.7 years ago by ▴ 10
1
vote
12
replies
3.0k
views
GSVA (running group samples separately)
GSVA
updated 4.7 years ago by ★ 3.4k • written 4.7 years ago by ▴ 30
1
vote
11
replies
3.1k
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 3.5 years ago by ▴ 10 • written 4.4 years ago by • 0
1
vote
2
replies
4.0k
views
GSVA error
GSVA
9 months ago Alex • 0
1
vote
2
replies
511
views
Interpretation of GSVA with absRanking=TRUE
GSVA
7 months ago gad.abraham • 0
1
vote
1
reply
1.8k
views
Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 2.8 years ago by ★ 3.4k • written 2.8 years ago by • 0
1
vote
2
replies
1.5k
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
3.4 years ago • updated 2.6 years ago Guandong Shang ▴ 40
1
vote
2
replies
475
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
5 weeks ago georgii.vdovin • 0
1
vote
4
replies
1.0k
views
GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment GSVA ssGSEA
updated 12 weeks ago by ▴ 10 • written 3 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish by brown.annaleigh • 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal by iqratechnology4 • 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Let me see if I can add some code to tximeta to cover this case. I've added an argument `skipRanges` in devel branch which should allow: …
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
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