Showing : GSVA • reset
1
vote
2
replies
230
views
GSVA error
GSVA
5 days ago • updated 4 days ago Alex • 0
1
vote
6
replies
430
views
GSVA on separate healthy and disease datasets
GSVA
updated 9 days ago by 65k • written 10 days ago by ▴ 60
2
votes
7
replies
1.7k
views
Issue with GSVA using dgCMatrix
GSVA
updated 6 weeks ago by ▴ 10 • written 2.8 years ago by • 0
9
votes
7
replies
20k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea gsva piano egsea
updated 4 months ago by ▴ 10 • written 6.7 years ago by ▴ 130
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 • 0 • written 14 months ago by • 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 ★ 3.2k • written 4 months ago by ▴ 20
0
votes
1
reply
383
views
GSVA exceeds 1
GSVA
updated 7 months ago by ★ 3.2k • written 7 months ago by • 0
3
votes
2
replies
1.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 9 months ago by 50k • written 9 months ago by ▴ 10
2
votes
0
replies
1.1k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
12 months ago Tadeoye ▴ 20
0
votes
2
replies
768
views
GSVA with and without absolute scaling method
GSVA
12 months ago arashdeep singh • 0
2
votes
4
replies
1.3k
views
Failed to install Biobase
GSVA Biobase
updated 12 months ago by 65k • written 12 months ago by • 0
0
votes
3
replies
712
views
GSVA: Error loading interactive web app
igsva GSVA
updated 14 months ago by ★ 3.2k • written 14 months ago by ▴ 40
0
votes
3
replies
1.0k
views
GSVA results interpretation
GSVA
updated 15 months ago by ★ 3.2k • written 15 months ago by • 0
0
votes
0
replies
700
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
15 months ago Zhijie • 0
0
votes
0
replies
748
views
Job: Research software engineer at UPF Barcelona
JobPosting Devel GSVA Software
17 months ago Robert Castelo ★ 3.2k
1
vote
5
replies
1.5k
views
'combined score' calculation with singscore vs gsva
singscore GSVA
17 months ago rocanja ▴ 60
0
votes
3
replies
1.8k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 17 months ago by ▴ 60 • written 21 months ago by • 0
0
votes
8
replies
5.5k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 19 months ago by ★ 3.2k • written 3.2 years ago by • 0
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
3
votes
4
replies
2.0k
views
Why Negative value from GSVA
GSVA RNASeq edgeR
21 months ago Yang Shi ▴ 10
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
2
votes
2
replies
1.3k
views
How to run GSVA with partially NA genes
GSVA
23 months ago blakebowen • 0
1
vote
3
replies
5.3k
views
GSVA and ssGSEA output differences
enrichment GSVA enrichplot ssGSEA
updated 2.0 years ago by ★ 3.2k • written 2.0 years ago by • 0
1
vote
1
reply
1.2k
views
Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 2.1 years ago by ★ 3.2k • written 2.1 years ago by • 0
0
votes
1
reply
772
views
Running PLAGE gets killed
GSVA SingleCellData
updated 2.1 years ago by ★ 3.2k • written 2.1 years ago by • 0
0
votes
1
reply
1.2k
views
GSVA: for a pathway, can enrichment scores of all samples be negative?
GSVAdata GSVA
updated 2.1 years ago by ★ 3.2k • written 2.1 years ago by • 0
0
votes
1
reply
1.2k
views
GSVA package normalization on gene-length ?
GSVA
updated 2.3 years ago by ★ 3.2k • written 2.3 years ago by • 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 ▴ 10 • written 3.7 years ago by • 0
2
votes
2
replies
2.0k
views
Questions regard to GSVA and Limma
limma GSVA
2.8 years ago Chenxi • 0
2
votes
2
replies
824
views
Turn of GSVA filtering for method ssGSEA
GSVA
2.8 years ago k.vitting.seerup ▴ 120
0
votes
1
reply
3.0k
views
GSVA Problem
GSVA
updated 2.9 years ago by ★ 3.2k • written 2.9 years ago by • 0
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
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 • 0 • written 5.1 years ago by ▴ 40
2
votes
3
replies
1.8k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 3.3 years ago by ★ 3.2k • written 3.3 years ago by ▴ 20
0
votes
3
replies
1.4k
views
GSVA on gene sets with 2 genes
GSVA gene sets RNA-seq
updated 3.5 years ago by ★ 3.2k • written 3.5 years ago by ▴ 70
0
votes
1
reply
1.1k
views
Extract GSVA gene rank matrix
gsva
updated 3.7 years ago by ★ 3.2k • written 3.7 years ago by • 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 ★ 3.2k • written 3.8 years ago by ▴ 40
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 ★ 3.2k • written 3.8 years ago by • 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 ★ 3.2k • written 3.8 years ago by ▴ 20
0
votes
1
reply
1.5k
views
GSVA on integrated/batch corrected scRNAseq data
GSVA Job
updated 3.9 years ago by ★ 3.2k • written 3.9 years ago by • 0
1
vote
12
replies
2.4k
views
GSVA (running group samples separately)
GSVA
updated 3.9 years ago by ★ 3.2k • written 3.9 years ago by ▴ 30
7
votes
11
replies
2.3k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.0 years ago by ★ 3.2k • written 4.0 years ago by ▴ 60
1
vote
1
reply
1.7k
views
Method and kcdf arguments in gsva package
GSVA
updated 4.0 years ago by ★ 3.2k • written 4.0 years ago by ▴ 10
1
vote
4
replies
4.9k
views
GSVA on RNAseq data
gsva rnaseq
updated 5.0 years ago by ★ 3.2k • written 5.0 years ago by ▴ 60
0
votes
1
reply
932
views
GSVA lots of positive values, is this expected behavior?
gsva
updated 5.0 years ago by ★ 3.2k • written 5.0 years ago by ▴ 10
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
5
votes
4
replies
3.0k
views
Differential expression on GSVA scores using LIMMA
limma gsva
updated 5.0 years ago by ★ 3.2k • written 5.0 years ago by ▴ 60
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
0
votes
0
replies
1.0k
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA geneset RNASeq TCGA subtypes
5.3 years ago Pietro ▴ 40
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
50 results • Page 1 of 1
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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…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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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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