Showing : GSVA • reset
0
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3
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78
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GSVA results interpretation
GSVA
updated 13 days ago by ★ 3.0k • written 14 days ago by • 0
0
votes
0
replies
53
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
22 days ago Zhijie • 0
0
votes
0
replies
117
views
Job: Research software engineer at UPF Barcelona
JobPosting Devel GSVA Software
9 weeks ago Robert Castelo ★ 3.0k
1
vote
5
replies
326
views
'combined score' calculation with singscore vs gsva
singscore GSVA
12 weeks ago • updated 10 weeks ago rocanja ▴ 60
5
votes
9
replies
664
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
6 months ago Yang Shi • 0
3
votes
4
replies
573
views
Why Negative value from GSVA
GSVA RNASeq edgeR
6 months ago Yang Shi • 0
0
votes
3
replies
454
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 12 weeks ago by ▴ 60 • written 6 months ago by • 0
1
vote
2
replies
433
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
17 months ago • updated 7 months ago Guandong Shang ▴ 40
2
votes
2
replies
345
views
How to run GSVA with partially NA genes
GSVA
8 months ago blakebowen • 0
1
vote
3
replies
1.7k
views
GSVA and ssGSEA output differences
enrichment GSVA enrichplot ssGSEA
updated 9 months ago by ★ 3.0k • written 9 months ago by • 0
1
vote
1
reply
345
views
Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 10 months ago by ★ 3.0k • written 10 months ago by • 0
0
votes
1
reply
336
views
Running PLAGE gets killed
GSVA SingleCellData
updated 10 months ago by ★ 3.0k • written 10 months ago by • 0
0
votes
1
reply
515
views
GSVA: for a pathway, can enrichment scores of all samples be negative?
GSVAdata GSVA
updated 10 months ago by ★ 3.0k • written 10 months ago by • 0
0
votes
1
reply
513
views
GSVA package normalization on gene-length ?
GSVA
updated 13 months ago by ★ 3.0k • written 13 months ago by • 0
1
vote
11
replies
1.7k
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 18 months ago by ▴ 10 • written 2.4 years ago by • 0
2
votes
2
replies
952
views
Questions regard to GSVA and Limma
limma GSVA
19 months ago Chenxi • 0
2
votes
2
replies
371
views
Turn of GSVA filtering for method ssGSEA
GSVA
19 months ago k.vitting.seerup ▴ 120
1
vote
2
replies
777
views
Issue with GSVA using dgCMatrix
GSVA
19 months ago resa • 0
0
votes
1
reply
1.2k
views
GSVA Problem
GSVA
updated 20 months ago by ★ 3.0k • written 20 months ago by • 0
6
votes
4
replies
939
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
23 months ago hanyin.wang88 ▴ 10
0
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8
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2.7k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 4 months ago by ★ 3.0k • written 23 months ago by • 0
2
votes
3
replies
1.1k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 2.1 years ago by ★ 3.0k • written 2.1 years ago by ▴ 20
0
votes
3
replies
733
views
GSVA on gene sets with 2 genes
GSVA gene sets RNA-seq
updated 2.2 years ago by ★ 3.0k • written 2.3 years ago by ▴ 60
0
votes
1
reply
578
views
Extract GSVA gene rank matrix
gsva
updated 2.5 years ago by ★ 3.0k • written 2.5 years ago by • 0
2
votes
1
reply
1.0k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 2.5 years ago by ★ 3.0k • written 2.5 years ago by ▴ 40
2
votes
2
replies
1.0k
views
Using GSVA All the pathway score are same
GSVA scRNA-seq data
updated 2.6 years ago by ★ 3.0k • written 2.6 years ago by • 0
2
votes
10
replies
2.1k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 2.6 years ago by ★ 3.0k • written 2.6 years ago by ▴ 20
0
votes
1
reply
756
views
GSVA on integrated/batch corrected scRNAseq data
GSVA Job
updated 2.7 years ago by ★ 3.0k • written 2.7 years ago by • 0
1
vote
12
replies
1.3k
views
GSVA (running group samples separately)
GSVA
updated 2.7 years ago by ★ 3.0k • written 2.7 years ago by ▴ 30
7
votes
11
replies
1.2k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 2.7 years ago by ★ 3.0k • written 2.7 years ago by ▴ 60
0
votes
1
reply
934
views
Method and kcdf arguments in gsva package
GSVA
updated 2.8 years ago by ★ 3.0k • written 2.8 years ago by ▴ 10
8
votes
6
replies
17k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea gsva piano egsea
updated 22 months ago by ▴ 10 • written 5.5 years ago by ▴ 120
1
vote
4
replies
3.1k
views
GSVA on RNAseq data
gsva rnaseq
updated 3.8 years ago by ★ 3.0k • written 3.8 years ago by ▴ 60
0
votes
1
reply
527
views
GSVA lots of positive values, is this expected behavior?
gsva
updated 3.8 years ago by ★ 3.0k • written 3.8 years ago by ▴ 10
1
vote
1
reply
948
views
GSVA with NanoString nCounter data
GSVA Nanostring
4.5 years ago • updated 3.8 years ago SB • 0
5
votes
4
replies
1.8k
views
Differential expression on GSVA scores using LIMMA
limma gsva
updated 3.8 years ago by ★ 3.0k • written 3.8 years ago by ▴ 60
2
votes
4
replies
1.4k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 2.1 years ago by • 0 • written 3.9 years ago by ▴ 40
10
votes
10
replies
4.1k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva gene set variation analysis normalization transformation rna-seq
4.8 years ago • updated 4.0 years ago rached ▴ 50
0
votes
0
replies
681
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA geneset RNASeq TCGA subtypes
4.0 years ago Pietro ▴ 40
1
vote
1
reply
761
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
4.1 years ago krassowski.michal ▴ 20
2
votes
1
reply
782
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA tutorial
updated 4.4 years ago by ★ 3.0k • written 4.4 years ago by ▴ 10
1
vote
4
replies
1.2k
views
Meaning of zero for ssGESA value calculated by GSVA package
gsva
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by • 0
2
votes
2
replies
1.1k
views
Input genes for GSVA
gsva gene expression matrix
updated 4.8 years ago by ★ 3.0k • written 4.8 years ago by ▴ 70
0
votes
4
replies
786
views
The selection of bandwidth of GSVA
GSVA gsva
updated 4.9 years ago by ★ 3.0k • written 4.9 years ago by • 0
1
vote
2
replies
1.4k
views
GSVA for single sample
gsea gsva ssgsea
5.0 years ago jaison75 ▴ 20
5
votes
16
replies
1.3k
views
GSVA package scores are opposite on mac and windows
GSVA bug gsva bugs
updated 5.3 years ago by ★ 3.0k • written 5.3 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Set rnaseq locial flag during GSVA
gsva rnaseq tpm
updated 5.4 years ago by ★ 3.0k • written 5.5 years ago by • 0
3
votes
2
replies
1.8k
views
GSVA: questions about the bootstrap p-value
gsva
updated 5.6 years ago by ★ 3.0k • written 5.6 years ago by ▴ 20
2
votes
9
replies
6.6k
views
Does GSVA enrichment score comes negative?
GSVA
6.6 years ago • updated 5.7 years ago pbachali ▴ 20
8
votes
3
replies
1.7k
views
GSVA indifferent to 'abs.ranking'
GSVA gsva abs.ranking
updated 5.7 years ago by ★ 3.0k • written 5.7 years ago by ▴ 120
50 results • Page 1 of 1
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Replies
Comment: transcript name mapping between human and mouse by Eric • 0
It works very well, and thanks for such a great answer! Because I use the old version gtf from GENECODE (vM12), the id version does not mat…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Bernardo • 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Votes
Answer: transcript name mapping between human and mouse
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
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