Showing : gsva • reset
1
vote
2
replies
401
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
9 days ago georgii.vdovin • 0
0
votes
4
replies
301
views
Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
updated 25 days ago by ★ 3.4k • written 4 weeks ago by • 0
1
vote
4
replies
879
views
GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment GSVA ssGSEA
updated 8 weeks ago by ▴ 10 • written 11 weeks ago by ▴ 10
0
votes
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
499
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
vote
4
replies
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
vote
2
replies
485
views
Interpretation of GSVA with absRanking=TRUE
GSVA
6 months ago gad.abraham • 0
0
votes
3
replies
943
views
GSVA function
DESeq2 GSVA ssGSEA
updated 6 months ago by ★ 3.4k • written 7 months ago by • 0
4
votes
5
replies
1.1k
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
7 months ago Chris ▴ 20
0
votes
0
replies
348
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
7 months ago Chris ▴ 20
1
vote
2
replies
3.7k
views
GSVA error
GSVA
8 months ago Alex • 0
1
vote
6
replies
919
views
GSVA on separate healthy and disease datasets
GSVA
updated 8 months ago by 67k • written 8 months ago by ▴ 60
4
votes
4
replies
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
votes
1
reply
648
views
GSVA exceeds 1
GSVA
updated 15 months ago by ★ 3.4k • written 16 months ago by • 0
4
votes
2
replies
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
votes
0
replies
1.8k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
20 months ago Tadeoye ▴ 20
0
votes
2
replies
1.1k
views
GSVA with and without absolute scaling method
GSVA
20 months ago arashdeep singh • 0
2
votes
4
replies
2.0k
views
Failed to install Biobase
GSVA Biobase
updated 21 months ago by 67k • written 21 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 12 months ago by • 0 • written 22 months ago by • 0
0
votes
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
votes
3
replies
1.8k
views
GSVA results interpretation
GSVA
updated 23 months ago by ★ 3.4k • written 23 months 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
23 months ago Zhijie • 0
1
vote
5
replies
2.1k
views
'combined score' calculation with singscore vs gsva
singscore GSVA
2.1 years ago rocanja ▴ 60
5
votes
9
replies
2.4k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.4 years ago Yang Shi ▴ 10
3
votes
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
vote
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
votes
2
replies
1.9k
views
How to run GSVA with partially NA genes
GSVA
2.6 years ago blakebowen • 0
1
vote
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
votes
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
reply
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
votes
2
replies
2.5k
views
Questions regard to GSVA and Limma
limma GSVA
3.5 years ago Chenxi • 0
2
votes
2
replies
1.0k
views
Turn of GSVA filtering for method ssGSEA
GSVA
3.5 years ago k.vitting.seerup ▴ 120
2
votes
7
replies
3.1k
views
Issue with GSVA using dgCMatrix
GSVA
updated 9 months ago by ▴ 10 • written 3.5 years ago by • 0
0
votes
1
reply
3.9k
views
GSVA Problem
GSVA
updated 3.6 years ago by ★ 3.4k • written 3.6 years ago by • 0
6
votes
4
replies
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
votes
8
replies
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
replies
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
votes
3
replies
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
votes
2
replies
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
replies
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
replies
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
Awards • All
Popular Question to Ali Barry ▴ 40
Popular Question to gabriel.hoffman ▴ 170
Popular Question to Jenny Drnevich ★ 2.0k
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
Locations • All
WEHI, Melbourne, Australia, 2 minutes ago
Germany, 2 hours ago
Barcelona/Universitat Pompeu Fabra, 2 hours ago
The city by the bay, 3 hours ago
China, 3 hours ago
Traffic: 1017 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6