Showing : gsva • reset
1
vote
2
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354
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 4 months ago by ▴ 10
1
vote
2
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1.4k
views
GSVA 1.52.2 (new API) nb of workers?
parallelize workers GSVA
written 18 months ago by • 0
1
vote
1
reply
2.0k
views
GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct" and "unused arguments (exprsData = as.matrix(rna_seq_sub), gset.idx…
GSVA
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
5
votes
5
replies
2.0k
views
Unused arguments error without used arguments in GSVA?
GSVA
updated 8 months ago by • 0 • written 10 months ago by • 0
1
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2
replies
1.2k
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
12 months ago georgii.vdovin • 0
1
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5
replies
1.3k
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 13 months ago by • 0
5
votes
4
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2.9k
views
GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment GSVA ssGSEA
updated 13 months ago by ▴ 10 • written 14 months ago by ▴ 30
0
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1
reply
1.6k
views
Job: Research software engineer at UPF Barcelona
JobPosting Devel GSVA Software
written 3.1 years ago by ★ 3.4k
0
votes
1
reply
1.2k
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea GSVA gsea
updated 16 months ago by ★ 1.1k • written 16 months ago by • 0
1
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4
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2.6k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
17 months ago Lucy ▴ 60
1
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2
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975
views
Interpretation of GSVA with absRanking=TRUE
GSVA
18 months ago gad.abraham • 0
0
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3
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2.0k
views
GSVA function
DESeq2 GSVA ssGSEA
updated 18 months ago by ★ 3.4k • written 19 months ago by • 0
4
votes
5
replies
2.0k
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
19 months ago Chris ▴ 20
0
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1
reply
1.2k
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
written 19 months ago by ▴ 20
1
vote
2
replies
6.2k
views
GSVA error
GSVA
20 months ago Alex • 0
1
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6
replies
1.5k
views
GSVA on separate healthy and disease datasets
GSVA
updated 20 months ago by 68k • written 20 months ago by ▴ 60
4
votes
4
replies
5.0k
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea GSVA biotype proteincoding msigdb
updated 14 months ago by • 0 • written 2.1 years ago by ▴ 200
0
votes
1
reply
966
views
GSVA exceeds 1
GSVA
updated 2.3 years ago by ★ 3.4k • written 2.3 years ago by • 0
4
votes
2
replies
3.3k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
2
votes
0
replies
2.6k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
2.7 years ago Tadeoye ▴ 20
0
votes
2
replies
1.6k
views
GSVA with and without absolute scaling method
GSVA
2.7 years ago arashdeep singh • 0
2
votes
4
replies
2.8k
views
Failed to install Biobase
GSVA Biobase
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
3
votes
6
replies
3.6k
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
escape UCell GSVA
updated 2.0 years ago by ▴ 10 • written 2.8 years ago by • 0
0
votes
3
replies
1.6k
views
GSVA: Error loading interactive web app
igsva GSVA
updated 2.8 years ago by ★ 3.4k • written 2.9 years ago by ▴ 40
0
votes
3
replies
2.8k
views
GSVA results interpretation
GSVA
updated 2.9 years ago by ★ 3.4k • written 2.9 years ago by • 0
0
votes
0
replies
1.4k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
3.0 years ago Zhijie • 0
1
vote
5
replies
2.9k
views
'combined score' calculation with singscore vs gsva
singscore GSVA
3.1 years ago rocanja ▴ 60
5
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9
replies
3.1k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
3.4 years ago Yang Shi ▴ 10
3
votes
4
replies
3.7k
views
Why Negative value from GSVA
GSVA RNASeq edgeR
3.5 years ago • updated 3.4 years ago Yang Shi ▴ 10
0
votes
3
replies
3.9k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 3.1 years ago by ▴ 60 • written 3.5 years ago by • 0
1
vote
2
replies
1.9k
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
4.3 years ago • updated 3.5 years ago Guandong Shang ▴ 40
2
votes
2
replies
2.5k
views
How to run GSVA with partially NA genes
GSVA
3.6 years ago blakebowen • 0
1
vote
3
replies
10k
views
GSVA and ssGSEA output differences
enrichment GSVA enrichplot ssGSEA
updated 3.7 years ago by ★ 3.4k • written 3.7 years ago by • 0
1
vote
1
reply
2.5k
views
Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 3.7 years ago by ★ 3.4k • written 3.7 years ago by • 0
0
votes
1
reply
1.2k
views
Running PLAGE gets killed
GSVA SingleCellData
updated 3.8 years ago by ★ 3.4k • written 3.8 years ago by • 0
0
votes
1
reply
2.2k
views
GSVA: for a pathway, can enrichment scores of all samples be negative?
GSVAdata GSVA
updated 3.8 years ago by ★ 3.4k • written 3.8 years ago by • 0
0
votes
1
reply
2.1k
views
GSVA package normalization on gene-length ?
GSVA
updated 4.0 years ago by ★ 3.4k • written 4.0 years ago by • 0
1
vote
11
replies
3.7k
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 4.4 years ago by ▴ 10 • written 5.3 years ago by • 0
2
votes
2
replies
3.1k
views
Questions regard to GSVA and Limma
limma GSVA
4.5 years ago Chenxi • 0
2
votes
2
replies
1.3k
views
Turn of GSVA filtering for method ssGSEA
GSVA
4.5 years ago k.vitting.seerup ▴ 120
2
votes
7
replies
4.8k
views
Issue with GSVA using dgCMatrix
GSVA
updated 21 months ago by ▴ 10 • written 4.5 years ago by • 0
0
votes
1
reply
4.7k
views
GSVA Problem
GSVA
updated 4.6 years ago by ★ 3.4k • written 4.6 years ago by • 0
6
votes
4
replies
2.5k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
4.9 years ago • updated 4.8 years ago hanyin.wang88 ▴ 10
0
votes
8
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9.2k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 3.2 years ago by ★ 3.4k • written 4.9 years ago by • 0
2
votes
3
replies
3.0k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 5.0 years ago by ★ 3.4k • written 5.0 years ago by ▴ 20
0
votes
3
replies
2.4k
views
GSVA on gene sets with 2 genes
GSVA gene sets RNA-seq
updated 5.1 years ago by ★ 3.4k • written 5.2 years ago by ▴ 70
0
votes
1
reply
1.8k
views
Extract GSVA gene rank matrix
gsva
updated 5.3 years ago by ★ 3.4k • written 5.3 years ago by • 0
2
votes
1
reply
3.5k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 5.4 years ago by ★ 3.4k • written 5.4 years ago by ▴ 50
2
votes
2
replies
2.7k
views
Using GSVA All the pathway score are same
GSVA scRNA-seq data
updated 5.5 years ago by ★ 3.4k • written 5.5 years ago by • 0
2
votes
10
replies
5.4k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 5.5 years ago by ★ 3.4k • written 5.5 years ago by ▴ 20
99 results • Page 1 of 2
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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