Showing : gsva • reset
1
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2
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475
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
5 weeks ago georgii.vdovin • 0
0
votes
5
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456
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 8 weeks ago by • 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
0
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1
reply
1.2k
views
Job: Research software engineer at UPF Barcelona
JobPosting Devel GSVA Software
written 2.2 years ago by ★ 3.4k
0
votes
1
reply
549
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea GSVA gsea
updated 5 months ago by ★ 1.0k • written 5 months ago by • 0
1
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4
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1.5k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
6 months ago Lucy ▴ 60
1
vote
1
reply
505
views
GSVA 1.52.2 (new API) nb of workers?
parallelize workers GSVA
updated 7 months ago by ★ 1.0k • written 7 months ago by • 0
1
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2
replies
511
views
Interpretation of GSVA with absRanking=TRUE
GSVA
7 months ago gad.abraham • 0
0
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3
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1.0k
views
GSVA function
DESeq2 GSVA ssGSEA
updated 7 months ago by ★ 3.4k • written 7 months ago by • 0
4
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5
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1.2k
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
8 months ago Chris ▴ 20
0
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0
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371
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Could we detect difference at pathway level but not significant different at gene level?
GSVA
8 months ago Chris ▴ 20
1
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2
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4.0k
views
GSVA error
GSVA
9 months ago Alex • 0
1
vote
6
replies
981
views
GSVA on separate healthy and disease datasets
GSVA
updated 9 months ago by 67k • written 9 months ago by ▴ 60
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
0
votes
1
reply
670
views
GSVA exceeds 1
GSVA
updated 16 months ago by ★ 3.4k • written 16 months ago by • 0
4
votes
2
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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
2
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0
replies
1.9k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
21 months ago Tadeoye ▴ 20
0
votes
2
replies
1.1k
views
GSVA with and without absolute scaling method
GSVA
21 months ago arashdeep singh • 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
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
0
votes
3
replies
1.1k
views
GSVA: Error loading interactive web app
igsva GSVA
updated 23 months ago by ★ 3.4k • written 23 months ago by ▴ 40
0
votes
3
replies
1.9k
views
GSVA results interpretation
GSVA
updated 2.0 years ago by ★ 3.4k • written 2.0 years ago by • 0
0
votes
0
replies
1.1k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
2.0 years ago Zhijie • 0
1
vote
5
replies
2.1k
views
'combined score' calculation with singscore vs gsva
singscore GSVA
2.2 years ago rocanja ▴ 60
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
3
votes
4
replies
2.8k
views
Why Negative value from GSVA
GSVA RNASeq edgeR
2.5 years ago Yang Shi ▴ 10
0
votes
3
replies
2.9k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 2.2 years ago by ▴ 60 • written 2.5 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
2
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2
replies
2.0k
views
How to run GSVA with partially NA genes
GSVA
2.7 years ago blakebowen • 0
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
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
0
votes
1
reply
1.0k
views
Running PLAGE gets killed
GSVA SingleCellData
updated 2.8 years ago by ★ 3.4k • written 2.8 years ago by • 0
0
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1
reply
1.7k
views
GSVA: for a pathway, can enrichment scores of all samples be negative?
GSVAdata GSVA
updated 2.9 years ago by ★ 3.4k • written 2.9 years ago by • 0
0
votes
1
reply
1.7k
views
GSVA package normalization on gene-length ?
GSVA
updated 3.1 years ago by ★ 3.4k • written 3.1 years ago by • 0
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
2
votes
2
replies
2.5k
views
Questions regard to GSVA and Limma
limma GSVA
3.6 years ago Chenxi • 0
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
0
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1
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4.0k
views
GSVA Problem
GSVA
updated 3.7 years ago by ★ 3.4k • written 3.7 years ago by • 0
6
votes
4
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2.1k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
3.9 years ago hanyin.wang88 ▴ 10
0
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8
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7.6k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 2.3 years ago by ★ 3.4k • written 3.9 years ago by • 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
0
votes
3
replies
1.9k
views
GSVA on gene sets with 2 genes
GSVA gene sets RNA-seq
updated 4.2 years ago by ★ 3.4k • written 4.3 years ago by ▴ 70
0
votes
1
reply
1.4k
views
Extract GSVA gene rank matrix
gsva
updated 4.4 years ago by ★ 3.4k • written 4.4 years 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
2.3k
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
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
0
votes
1
reply
1.8k
views
GSVA on integrated/batch corrected scRNAseq data
GSVA Job
updated 4.6 years ago by ★ 3.4k • written 4.6 years ago by • 0
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
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
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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