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GSVA
•
reset
0
votes
0
replies
12
views
GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment
GSVA
ssGSEA
8 hours ago
Bob
• 0
0
votes
1
reply
1.0k
views
Job:
Research software engineer at UPF Barcelona
JobPosting
Devel
GSVA
Software
written 22 months ago by
Robert Castelo
★ 3.4k
0
votes
1
reply
341
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea
GSVA
gsea
updated 8 weeks ago by
Axel Klenk
★ 1.0k • written 8 weeks ago by
Bioinformagician
• 0
1
vote
4
replies
1.2k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA
GSVAdata
RNAseq
12 weeks ago • updated 10 weeks ago
Lucy
▴ 60
1
vote
1
reply
351
views
GSVA 1.52.2 (new API) nb of workers?
parallelize
workers
GSVA
updated 3 months ago by
Axel Klenk
★ 1.0k • written 3 months ago by
johanna.galvis
• 0
1
vote
2
replies
389
views
Interpretation of GSVA with absRanking=TRUE
GSVA
4 months ago • updated 3 months ago
gad.abraham
• 0
0
votes
3
replies
608
views
GSVA function
DESeq2
GSVA
ssGSEA
updated 4 months ago by
Robert Castelo
★ 3.4k • written 4 months ago by
michelafrancesconi8
• 0
4
votes
5
replies
828
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
5 months ago • updated 4 months ago
Chris
▴ 20
0
votes
0
replies
261
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
5 months ago
Chris
▴ 20
1
vote
2
replies
2.6k
views
GSVA error
GSVA
5 months ago
Alex
• 0
1
vote
6
replies
773
views
GSVA on separate healthy and disease datasets
GSVA
updated 5 months ago by
James W. MacDonald
67k • written 5 months ago by
Lucy
▴ 60
4
votes
4
replies
1.6k
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 7 days ago by
Ginny
• 0 • written 10 months ago by
snijesh
▴ 200
0
votes
1
reply
578
views
GSVA exceeds 1
GSVA
updated 13 months ago by
Robert Castelo
★ 3.4k • written 13 months ago by
Heba
• 0
4
votes
2
replies
1.8k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 15 months ago by
Gordon Smyth
51k • written 15 months ago by
Jonathan
▴ 10
2
votes
0
replies
1.6k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
18 months ago
Tadeoye
▴ 20
0
votes
2
replies
989
views
GSVA with and without absolute scaling method
GSVA
18 months ago
arashdeep singh
• 0
2
votes
4
replies
1.8k
views
Failed to install Biobase
GSVA
Biobase
updated 18 months ago by
James W. MacDonald
67k • written 18 months ago by
johann.brisseau
• 0
2
votes
6
replies
2.2k
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
escape
UCell
GSVA
updated 10 months ago by
arina
• 0 • written 19 months ago by
Omer
• 0
0
votes
3
replies
953
views
GSVA: Error loading interactive web app
igsva
GSVA
updated 19 months ago by
Robert Castelo
★ 3.4k • written 20 months ago by
sharvari gujja
▴ 40
0
votes
3
replies
1.6k
views
GSVA results interpretation
GSVA
updated 21 months ago by
Robert Castelo
★ 3.4k • written 21 months ago by
munta.jihad
• 0
0
votes
0
replies
986
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
21 months ago
Zhijie
• 0
1
vote
5
replies
1.9k
views
'combined score' calculation with singscore vs gsva
singscore
GSVA
23 months ago
rocanja
▴ 60
5
votes
9
replies
2.2k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
2.2 years ago
Yang Shi
▴ 10
3
votes
4
replies
2.5k
views
Why Negative value from GSVA
GSVA
RNASeq
edgeR
2.2 years ago
Yang Shi
▴ 10
0
votes
3
replies
2.5k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA
GSVA
updated 23 months ago by
rocanja
▴ 60 • written 2.3 years ago by
João
• 0
1
vote
2
replies
1.3k
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
3.1 years ago • updated 2.3 years ago
Guandong Shang
▴ 40
2
votes
2
replies
1.7k
views
How to run GSVA with partially NA genes
GSVA
2.4 years ago
blakebowen
• 0
1
vote
3
replies
6.9k
views
GSVA and ssGSEA output differences
enrichment
GSVA
enrichplot
ssGSEA
updated 2.5 years ago by
Robert Castelo
★ 3.4k • written 2.5 years ago by
Davide
• 0
1
vote
1
reply
1.6k
views
Cleaning GeneSets from GSEA
msigdb
GSEABase
GSVA
updated 2.5 years ago by
Robert Castelo
★ 3.4k • written 2.5 years ago by
forlani.luca
• 0
0
votes
1
reply
943
views
Running PLAGE gets killed
GSVA
SingleCellData
updated 2.6 years ago by
Robert Castelo
★ 3.4k • written 2.6 years ago by
Amna
• 0
0
votes
1
reply
1.5k
views
GSVA: for a pathway, can enrichment scores of all samples be negative?
GSVAdata
GSVA
updated 2.6 years ago by
Robert Castelo
★ 3.4k • written 2.6 years ago by
random
• 0
0
votes
1
reply
1.5k
views
GSVA package normalization on gene-length ?
GSVA
updated 2.8 years ago by
Robert Castelo
★ 3.4k • written 2.8 years ago by
xanthexu
• 0
1
vote
11
replies
2.9k
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 3.2 years ago by
soudayo
▴ 10 • written 4.1 years ago by
yaoxucpu
• 0
2
votes
2
replies
2.3k
views
Questions regard to GSVA and Limma
limma
GSVA
3.3 years ago
Chenxi
• 0
2
votes
2
replies
993
views
Turn of GSVA filtering for method ssGSEA
GSVA
3.3 years ago
k.vitting.seerup
▴ 120
2
votes
7
replies
2.4k
views
Issue with GSVA using dgCMatrix
GSVA
updated 7 months ago by
Moritz
▴ 10 • written 3.3 years ago by
resa
• 0
0
votes
1
reply
3.5k
views
GSVA Problem
GSVA
updated 3.4 years ago by
Robert Castelo
★ 3.4k • written 3.4 years ago by
tywzlzl2011
• 0
6
votes
4
replies
1.9k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
3.7 years ago • updated 3.6 years ago
hanyin.wang88
▴ 10
0
votes
8
replies
6.7k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 2.0 years ago by
Robert Castelo
★ 3.4k • written 3.7 years ago by
Siyuan
• 0
2
votes
3
replies
2.1k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 3.8 years ago by
Robert Castelo
★ 3.4k • written 3.8 years ago by
hsiowa2
▴ 20
0
votes
3
replies
1.7k
views
GSVA on gene sets with 2 genes
GSVA
gene sets
RNA-seq
updated 3.9 years ago by
Robert Castelo
★ 3.4k • written 4.0 years ago by
Endre Sebestyén
▴ 70
0
votes
1
reply
1.4k
views
Extract GSVA gene rank matrix
gsva
updated 4.1 years ago by
Robert Castelo
★ 3.4k • written 4.1 years ago by
dylan
• 0
2
votes
1
reply
2.5k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 4.2 years ago by
Robert Castelo
★ 3.4k • written 4.2 years ago by
igor
▴ 50
2
votes
2
replies
2.1k
views
Using GSVA All the pathway score are same
GSVA
scRNA-seq data
updated 4.3 years ago by
Robert Castelo
★ 3.4k • written 4.3 years ago by
initialqy
• 0
2
votes
10
replies
4.2k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 4.3 years ago by
Robert Castelo
★ 3.4k • written 4.3 years ago by
hsiowa2
▴ 20
0
votes
1
reply
1.7k
views
GSVA on integrated/batch corrected scRNAseq data
GSVA
Job
updated 4.4 years ago by
Robert Castelo
★ 3.4k • written 4.4 years ago by
laura.derooij
• 0
1
vote
12
replies
2.8k
views
GSVA (running group samples separately)
GSVA
updated 4.4 years ago by
Robert Castelo
★ 3.4k • written 4.4 years ago by
Jenn
▴ 30
7
votes
11
replies
2.9k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 4.4 years ago by
Robert Castelo
★ 3.4k • written 4.4 years ago by
rocanja
▴ 60
1
vote
1
reply
2.0k
views
Method and kcdf arguments in gsva package
GSVA
updated 4.4 years ago by
Robert Castelo
★ 3.4k • written 4.4 years ago by
thkapell
▴ 10
9
votes
7
replies
20k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea
gsva
piano
egsea
updated 10 months ago by
amin8w
▴ 10 • written 7.2 years ago by
sina.nassiri
▴ 130
50 results • Page
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mercedeh.movassagh
▴ 20
Hi Maria, so what is the code you are using? By the 3rd way to conduct the analysis do you mean looking at the interaction model from part …
Comment: miRTarRnaseq library
by
María Calvo
• 0
Hello, in line with the previous questions, when the miRNA-mRNA interaction analysis is performed (3 rd way to conduct the analysis), I obt…
Answer: heatmap with batch effect
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James W. MacDonald
67k
You have only one condition in the second batch, so it's not possible to remove the batch effect. You can probably adjust for it somewhat, …
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67k
``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame with 865859 rows and 3 columns ch…
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Not too familiar with SCT v2. If it also has a point-mass at zero and the non-zero component is roughly-symmetric, then it might work ok w…
Votes
Answer: How to control batch effect if Group and batch are same?
Answer: How to control batch effect if Group and batch are same?
Answer: How to control batch effect if Group and batch are same?
Comment: Convert HGVS Representation back to Reference Genome Coordinates
Answer: How to control batch effect if Group and batch are same?
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