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gsva
•
reset
1
vote
2
replies
359
views
GSVA error
GSVA
11 days ago • updated 9 days ago
Alex
• 0
1
vote
6
replies
454
views
GSVA on separate healthy and disease datasets
GSVA
updated 14 days ago by
James W. MacDonald
65k • written 15 days ago by
Lucy
▴ 60
1
vote
1
reply
591
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 4 months ago by
Robert Castelo
★ 3.3k • written 4 months ago by
snijesh
▴ 20
0
votes
1
reply
392
views
GSVA exceeds 1
GSVA
updated 7 months ago by
Robert Castelo
★ 3.3k • written 8 months ago by
Heba
• 0
4
votes
2
replies
1.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
Jonathan
▴ 10
2
votes
0
replies
1.1k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
12 months ago
Tadeoye
▴ 20
0
votes
2
replies
778
views
GSVA with and without absolute scaling method
GSVA
12 months ago
arashdeep singh
• 0
2
votes
4
replies
1.3k
views
Failed to install Biobase
GSVA
Biobase
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
johann.brisseau
• 0
2
votes
6
replies
1.6k
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
escape
UCell
GSVA
updated 4 months ago by
arina
• 0 • written 14 months ago by
Omer
• 0
0
votes
3
replies
724
views
GSVA: Error loading interactive web app
igsva
GSVA
updated 14 months ago by
Robert Castelo
★ 3.3k • written 14 months ago by
sharvari gujja
▴ 40
0
votes
3
replies
1.0k
views
GSVA results interpretation
GSVA
updated 15 months ago by
Robert Castelo
★ 3.3k • written 15 months ago by
munta.jihad
• 0
0
votes
0
replies
716
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
15 months ago
Zhijie
• 0
0
votes
0
replies
756
views
Job:
Research software engineer at UPF Barcelona
JobPosting
Devel
GSVA
Software
17 months ago
Robert Castelo
★ 3.3k
1
vote
5
replies
1.5k
views
'combined score' calculation with singscore vs gsva
singscore
GSVA
17 months ago
rocanja
▴ 60
5
votes
9
replies
1.8k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
21 months ago
Yang Shi
▴ 10
3
votes
4
replies
2.0k
views
Why Negative value from GSVA
GSVA
RNASeq
edgeR
21 months ago
Yang Shi
▴ 10
0
votes
3
replies
1.8k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA
GSVA
updated 17 months ago by
rocanja
▴ 60 • written 21 months ago by
João
• 0
1
vote
2
replies
1.1k
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
2.7 years ago • updated 23 months ago
Guandong Shang
▴ 40
2
votes
2
replies
1.3k
views
How to run GSVA with partially NA genes
GSVA
23 months ago
blakebowen
• 0
1
vote
3
replies
5.4k
views
GSVA and ssGSEA output differences
enrichment
GSVA
enrichplot
ssGSEA
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 2.1 years ago by
Davide
• 0
1
vote
1
reply
1.2k
views
Cleaning GeneSets from GSEA
msigdb
GSEABase
GSVA
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 2.1 years ago by
forlani.luca
• 0
0
votes
1
reply
779
views
Running PLAGE gets killed
GSVA
SingleCellData
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 2.1 years ago by
Amna
• 0
0
votes
1
reply
1.2k
views
GSVA: for a pathway, can enrichment scores of all samples be negative?
GSVAdata
GSVA
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 2.1 years ago by
random
• 0
0
votes
1
reply
1.2k
views
GSVA package normalization on gene-length ?
GSVA
updated 2.4 years ago by
Robert Castelo
★ 3.3k • written 2.4 years ago by
xanthexu
• 0
1
vote
11
replies
2.7k
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 2.8 years ago by
soudayo
▴ 10 • written 3.7 years ago by
yaoxucpu
• 0
2
votes
2
replies
2.0k
views
Questions regard to GSVA and Limma
limma
GSVA
2.8 years ago
Chenxi
• 0
2
votes
2
replies
830
views
Turn of GSVA filtering for method ssGSEA
GSVA
2.8 years ago
k.vitting.seerup
▴ 120
2
votes
7
replies
1.8k
views
Issue with GSVA using dgCMatrix
GSVA
updated 7 weeks ago by
Moritz
▴ 10 • written 2.9 years ago by
resa
• 0
0
votes
1
reply
3.0k
views
GSVA Problem
GSVA
updated 2.9 years ago by
Robert Castelo
★ 3.3k • written 2.9 years ago by
tywzlzl2011
• 0
6
votes
4
replies
1.7k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
3.2 years ago
hanyin.wang88
▴ 10
0
votes
8
replies
5.6k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 19 months ago by
Robert Castelo
★ 3.3k • written 3.2 years ago by
Siyuan
• 0
2
votes
3
replies
1.8k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 3.3 years ago by
Robert Castelo
★ 3.3k • written 3.3 years ago by
hsiowa2
▴ 20
0
votes
3
replies
1.4k
views
GSVA on gene sets with 2 genes
GSVA
gene sets
RNA-seq
updated 3.5 years ago by
Robert Castelo
★ 3.3k • written 3.5 years ago by
Endre Sebestyén
▴ 70
0
votes
1
reply
1.1k
views
Extract GSVA gene rank matrix
gsva
updated 3.7 years ago by
Robert Castelo
★ 3.3k • written 3.7 years ago by
dylan
• 0
2
votes
1
reply
2.0k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 3.8 years ago by
Robert Castelo
★ 3.3k • written 3.8 years ago by
igor
▴ 40
2
votes
2
replies
1.8k
views
Using GSVA All the pathway score are same
GSVA
scRNA-seq data
updated 3.8 years ago by
Robert Castelo
★ 3.3k • written 3.8 years ago by
initialqy
• 0
2
votes
10
replies
3.6k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 3.8 years ago by
Robert Castelo
★ 3.3k • written 3.8 years ago by
hsiowa2
▴ 20
0
votes
1
reply
1.5k
views
GSVA on integrated/batch corrected scRNAseq data
GSVA
Job
updated 3.9 years ago by
Robert Castelo
★ 3.3k • written 3.9 years ago by
laura.derooij
• 0
1
vote
12
replies
2.4k
views
GSVA (running group samples separately)
GSVA
updated 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
Jenn
▴ 30
7
votes
11
replies
2.4k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
rocanja
▴ 60
1
vote
1
reply
1.7k
views
Method and kcdf arguments in gsva package
GSVA
updated 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 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 4 months ago by
amin8w
▴ 10 • written 6.8 years ago by
sina.nassiri
▴ 130
1
vote
4
replies
5.0k
views
GSVA on RNAseq data
gsva
rnaseq
updated 5.0 years ago by
Robert Castelo
★ 3.3k • written 5.0 years ago by
rocanja
▴ 60
0
votes
1
reply
940
views
GSVA lots of positive values, is this expected behavior?
gsva
updated 5.0 years ago by
Robert Castelo
★ 3.3k • written 5.0 years ago by
owen.whitley
▴ 10
1
vote
1
reply
1.4k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
5.8 years ago • updated 5.1 years ago
SB
• 0
5
votes
4
replies
3.1k
views
Differential expression on GSVA scores using LIMMA
limma
gsva
updated 5.1 years ago by
Robert Castelo
★ 3.3k • written 5.1 years ago by
rocanja
▴ 60
2
votes
4
replies
2.4k
views
Are singscore scores comparable between gene sets?
singscore
GSVA
GSEA
subtypes
geneset
updated 3.3 years ago by
Dharmesh D Bhuva
• 0 • written 5.1 years ago by
Pietro
▴ 40
12
votes
10
replies
6.5k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva
gene set variation analysis
normalization
transformation
rna-seq
6.1 years ago • updated 5.3 years ago
rached
▴ 60
0
votes
0
replies
1.0k
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA
geneset
RNASeq
TCGA
subtypes
5.3 years ago
Pietro
▴ 40
1
vote
1
reply
1.3k
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
5.3 years ago
krassowski.michal
▴ 40
50 results • Page
1 of 1
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Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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