Showing : GSVA • reset
1
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2
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402
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
9 days ago georgii.vdovin • 0
0
votes
4
replies
302
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
updated 26 days ago by ★ 3.4k • written 4 weeks ago by • 0
1
vote
4
replies
882
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GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment GSVA ssGSEA
updated 8 weeks ago by ▴ 10 • written 11 weeks 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 2.1 years ago by ★ 3.4k
0
votes
1
reply
500
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea GSVA gsea
updated 4 months ago by ★ 1.0k • written 4 months ago by • 0
1
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4
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1.4k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
5 months ago Lucy ▴ 60
1
vote
1
reply
459
views
GSVA 1.52.2 (new API) nb of workers?
parallelize workers GSVA
updated 6 months ago by ★ 1.0k • written 6 months ago by • 0
1
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2
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485
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Interpretation of GSVA with absRanking=TRUE
GSVA
6 months ago gad.abraham • 0
0
votes
3
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943
views
GSVA function
DESeq2 GSVA ssGSEA
updated 6 months ago by ★ 3.4k • written 7 months ago by • 0
4
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5
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1.1k
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
7 months ago Chris ▴ 20
0
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0
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348
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Could we detect difference at pathway level but not significant different at gene level?
GSVA
7 months ago Chris ▴ 20
1
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2
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3.7k
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GSVA error
GSVA
8 months ago Alex • 0
1
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6
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920
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GSVA on separate healthy and disease datasets
GSVA
updated 8 months ago by 67k • written 8 months ago by ▴ 60
4
votes
4
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2.3k
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea GSVA biotype proteincoding msigdb
updated 12 weeks ago by • 0 • written 12 months ago by ▴ 200
0
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1
reply
649
views
GSVA exceeds 1
GSVA
updated 15 months ago by ★ 3.4k • written 16 months ago by • 0
4
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2
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2.1k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 17 months ago by 52k • written 17 months ago by ▴ 10
2
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0
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1.8k
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How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
20 months ago Tadeoye ▴ 20
0
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2
replies
1.1k
views
GSVA with and without absolute scaling method
GSVA
20 months ago arashdeep singh • 0
2
votes
4
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2.0k
views
Failed to install Biobase
GSVA Biobase
updated 21 months ago by 67k • written 21 months ago by • 0
2
votes
6
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2.5k
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
escape UCell GSVA
updated 12 months ago by • 0 • written 22 months ago by • 0
0
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3
replies
1.1k
views
GSVA: Error loading interactive web app
igsva GSVA
updated 22 months ago by ★ 3.4k • written 22 months ago by ▴ 40
0
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3
replies
1.8k
views
GSVA results interpretation
GSVA
updated 23 months ago by ★ 3.4k • written 23 months ago by • 0
0
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0
replies
1.1k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
23 months ago Zhijie • 0
1
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5
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2.1k
views
'combined score' calculation with singscore vs gsva
singscore GSVA
2.1 years ago rocanja ▴ 60
5
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9
replies
2.4k
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GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.4 years ago Yang Shi ▴ 10
3
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4
replies
2.7k
views
Why Negative value from GSVA
GSVA RNASeq edgeR
2.5 years ago Yang Shi ▴ 10
0
votes
3
replies
2.8k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 2.1 years ago by ▴ 60 • written 2.5 years ago by • 0
1
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2
replies
1.5k
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
3.3 years ago • updated 2.6 years ago Guandong Shang ▴ 40
2
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2
replies
1.9k
views
How to run GSVA with partially NA genes
GSVA
2.6 years ago blakebowen • 0
1
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3
replies
7.8k
views
GSVA and ssGSEA output differences
enrichment GSVA enrichplot ssGSEA
updated 2.7 years ago by ★ 3.4k • written 2.7 years ago by • 0
1
vote
1
reply
1.8k
views
Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 2.7 years ago by ★ 3.4k • written 2.7 years ago by • 0
0
votes
1
reply
991
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
1.6k
views
GSVA: for a pathway, can enrichment scores of all samples be negative?
GSVAdata GSVA
updated 2.8 years ago by ★ 3.4k • written 2.8 years ago by • 0
0
votes
1
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1.6k
views
GSVA package normalization on gene-length ?
GSVA
updated 3.0 years ago by ★ 3.4k • written 3.0 years ago by • 0
1
vote
11
replies
3.0k
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 3.4 years ago by ▴ 10 • written 4.3 years ago by • 0
2
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2
replies
2.5k
views
Questions regard to GSVA and Limma
limma GSVA
3.5 years ago Chenxi • 0
2
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2
replies
1.0k
views
Turn of GSVA filtering for method ssGSEA
GSVA
3.5 years ago k.vitting.seerup ▴ 120
2
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7
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3.1k
views
Issue with GSVA using dgCMatrix
GSVA
updated 9 months ago by ▴ 10 • written 3.5 years ago by • 0
0
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1
reply
3.9k
views
GSVA Problem
GSVA
updated 3.6 years ago by ★ 3.4k • written 3.6 years ago by • 0
6
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4
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2.0k
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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7.4k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 2.2 years ago by ★ 3.4k • written 3.9 years ago by • 0
2
votes
3
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2.3k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 4.0 years ago by ★ 3.4k • written 4.0 years ago by ▴ 20
0
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3
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1.8k
views
GSVA on gene sets with 2 genes
GSVA gene sets RNA-seq
updated 4.1 years ago by ★ 3.4k • written 4.2 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 4.4 years ago by ★ 3.4k • written 4.4 years ago by ▴ 50
2
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2
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2.2k
views
Using GSVA All the pathway score are same
GSVA scRNA-seq data
updated 4.5 years ago by ★ 3.4k • written 4.5 years ago by • 0
2
votes
10
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4.4k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 4.5 years ago by ★ 3.4k • written 4.5 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
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3.0k
views
GSVA (running group samples separately)
GSVA
updated 4.6 years ago by ★ 3.4k • written 4.6 years ago by ▴ 30
7
votes
11
replies
3.1k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.6 years ago by ★ 3.4k • written 4.6 years ago by ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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