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gsva
•
reset
1
vote
2
replies
516
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
7 weeks ago
georgii.vdovin
• 0
0
votes
5
replies
528
views
Identifying potentially associated gene set to drug response using GSVA
drug
RNASeq
GSVA
written 10 weeks ago by
Kent
• 0
1
vote
4
replies
1.1k
views
GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment
GSVA
ssGSEA
updated 3 months ago by
Tyler Sagendorf
▴ 10 • written 3 months ago by
Bob
▴ 10
0
votes
1
reply
1.2k
views
Job:
Research software engineer at UPF Barcelona
JobPosting
Devel
GSVA
Software
written 2.2 years ago by
Robert Castelo
★ 3.4k
0
votes
1
reply
584
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea
GSVA
gsea
updated 5 months ago by
Axel Klenk
★ 1.0k • written 5 months ago by
Bioinformagician
• 0
1
vote
4
replies
1.6k
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
530
views
GSVA 1.52.2 (new API) nb of workers?
parallelize
workers
GSVA
updated 7 months ago by
Axel Klenk
★ 1.0k • written 7 months ago by
johanna.galvis
• 0
1
vote
2
replies
534
views
Interpretation of GSVA with absRanking=TRUE
GSVA
7 months ago
gad.abraham
• 0
0
votes
3
replies
1.1k
views
GSVA function
DESeq2
GSVA
ssGSEA
updated 8 months ago by
Robert Castelo
★ 3.4k • written 8 months ago by
michelafrancesconi8
• 0
4
votes
5
replies
1.2k
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
8 months ago
Chris
▴ 20
0
votes
0
replies
385
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
9 months ago
Chris
▴ 20
1
vote
2
replies
4.2k
views
GSVA error
GSVA
9 months ago
Alex
• 0
1
vote
6
replies
1.0k
views
GSVA on separate healthy and disease datasets
GSVA
updated 9 months ago by
James W. MacDonald
67k • written 9 months ago by
Lucy
▴ 60
4
votes
4
replies
2.6k
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 4 months ago by
Ginny
• 0 • written 14 months ago by
snijesh
▴ 200
0
votes
1
reply
681
views
GSVA exceeds 1
GSVA
updated 17 months ago by
Robert Castelo
★ 3.4k • written 17 months ago by
Heba
• 0
4
votes
2
replies
2.3k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 19 months ago by
Gordon Smyth
52k • written 19 months ago by
Jonathan
▴ 10
2
votes
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
22 months ago • updated 21 months ago
arashdeep singh
• 0
2
votes
4
replies
2.1k
views
Failed to install Biobase
GSVA
Biobase
updated 22 months ago by
James W. MacDonald
67k • written 22 months ago by
johann.brisseau
• 0
2
votes
6
replies
2.6k
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
escape
UCell
GSVA
updated 14 months ago by
arina
• 0 • written 23 months ago by
Omer
• 0
0
votes
3
replies
1.1k
views
GSVA: Error loading interactive web app
igsva
GSVA
updated 23 months ago by
Robert Castelo
★ 3.4k • written 24 months ago by
sharvari gujja
▴ 40
0
votes
3
replies
2.0k
views
GSVA results interpretation
GSVA
updated 2.0 years ago by
Robert Castelo
★ 3.4k • written 2.1 years ago by
munta.jihad
• 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
2.1 years ago
Zhijie
• 0
1
vote
5
replies
2.2k
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
2.6 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
rocanja
▴ 60 • written 2.6 years ago by
João
• 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 2.7 years ago
Guandong Shang
▴ 40
2
votes
2
replies
2.0k
views
How to run GSVA with partially NA genes
GSVA
2.7 years ago
blakebowen
• 0
1
vote
3
replies
8.3k
views
GSVA and ssGSEA output differences
enrichment
GSVA
enrichplot
ssGSEA
updated 2.8 years ago by
Robert Castelo
★ 3.4k • written 2.8 years ago by
Davide
• 0
1
vote
1
reply
1.9k
views
Cleaning GeneSets from GSEA
msigdb
GSEABase
GSVA
updated 2.8 years ago by
Robert Castelo
★ 3.4k • written 2.8 years ago by
forlani.luca
• 0
0
votes
1
reply
1.0k
views
Running PLAGE gets killed
GSVA
SingleCellData
updated 2.9 years ago by
Robert Castelo
★ 3.4k • written 2.9 years ago by
Amna
• 0
0
votes
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
Robert Castelo
★ 3.4k • written 2.9 years ago by
random
• 0
0
votes
1
reply
1.7k
views
GSVA package normalization on gene-length ?
GSVA
updated 3.1 years ago by
Robert Castelo
★ 3.4k • written 3.1 years ago by
xanthexu
• 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
soudayo
▴ 10 • written 4.4 years ago by
yaoxucpu
• 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
3.3k
views
Issue with GSVA using dgCMatrix
GSVA
updated 11 months ago by
Moritz
▴ 10 • written 3.6 years ago by
resa
• 0
0
votes
1
reply
4.1k
views
GSVA Problem
GSVA
updated 3.7 years ago by
Robert Castelo
★ 3.4k • written 3.7 years ago by
tywzlzl2011
• 0
6
votes
4
replies
2.1k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
4.0 years ago
hanyin.wang88
▴ 10
0
votes
8
replies
7.7k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 2.4 years ago by
Robert Castelo
★ 3.4k • written 4.0 years ago by
Siyuan
• 0
2
votes
3
replies
2.4k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 4.1 years ago by
Robert Castelo
★ 3.4k • written 4.1 years ago by
hsiowa2
▴ 20
0
votes
3
replies
1.9k
views
GSVA on gene sets with 2 genes
GSVA
gene sets
RNA-seq
updated 4.3 years ago by
Robert Castelo
★ 3.4k • written 4.3 years ago by
Endre Sebestyén
▴ 70
0
votes
1
reply
1.5k
views
Extract GSVA gene rank matrix
gsva
updated 4.5 years ago by
Robert Castelo
★ 3.4k • written 4.5 years ago by
dylan
• 0
2
votes
1
reply
2.8k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 4.6 years ago by
Robert Castelo
★ 3.4k • written 4.6 years ago by
igor
▴ 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
Robert Castelo
★ 3.4k • written 4.6 years ago by
initialqy
• 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
Robert Castelo
★ 3.4k • written 4.6 years ago by
hsiowa2
▴ 20
0
votes
1
reply
1.9k
views
GSVA on integrated/batch corrected scRNAseq data
GSVA
Job
updated 4.7 years ago by
Robert Castelo
★ 3.4k • written 4.7 years ago by
laura.derooij
• 0
1
vote
12
replies
3.1k
views
GSVA (running group samples separately)
GSVA
updated 4.7 years ago by
Robert Castelo
★ 3.4k • written 4.7 years ago by
Jenn
▴ 30
7
votes
11
replies
3.2k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 4.8 years ago by
Robert Castelo
★ 3.4k • written 4.8 years ago by
rocanja
▴ 60
50 results • Page
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Comment: input for singR function
by
iamin053
• 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Comment: build samplesheet and plot profile
by
yf
• 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Votes
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
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