Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
GSVA
•
reset
0
votes
0
replies
162
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
7 weeks ago
Tadeoye
• 0
0
votes
2
replies
175
views
GSVA with and without absolute scaling method
GSVA
7 weeks ago
arashdeep singh
• 0
2
votes
4
replies
490
views
Failed to install Biobase
GSVA
Biobase
updated 9 weeks ago by
James W. MacDonald
63k • written 9 weeks ago by
johann.brisseau
• 0
2
votes
5
replies
391
views
How can I avoid artifacts in gene set/pathway scoring by UCell and similar algorithms?
escape
UCell
GSVA
3 months ago
Omer
• 0
0
votes
3
replies
234
views
GSVA: Error loading interactive web app
igsva
GSVA
updated 3 months ago by
Robert Castelo
★ 3.0k • written 3 months ago by
sharvari gujja
▴ 40
0
votes
3
replies
246
views
GSVA results interpretation
GSVA
updated 4 months ago by
Robert Castelo
★ 3.0k • written 4 months ago by
munta.jihad
• 0
0
votes
0
replies
173
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
5 months ago
Zhijie
• 0
0
votes
0
replies
286
views
Job:
Research software engineer at UPF Barcelona
JobPosting
Devel
GSVA
Software
6 months ago
Robert Castelo
★ 3.0k
1
vote
5
replies
594
views
'combined score' calculation with singscore vs gsva
singscore
GSVA
7 months ago • updated 6 months ago
rocanja
▴ 60
5
votes
9
replies
922
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
10 months ago
Yang Shi
▴ 10
3
votes
4
replies
951
views
Why Negative value from GSVA
GSVA
RNASeq
edgeR
11 months ago
Yang Shi
▴ 10
0
votes
3
replies
743
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA
GSVA
updated 7 months ago by
rocanja
▴ 60 • written 11 months ago by
João
• 0
1
vote
2
replies
577
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
21 months ago • updated 12 months ago
Guandong Shang
▴ 40
2
votes
2
replies
569
views
How to run GSVA with partially NA genes
GSVA
12 months ago
blakebowen
• 0
1
vote
3
replies
2.8k
views
GSVA and ssGSEA output differences
enrichment
GSVA
enrichplot
ssGSEA
updated 14 months ago by
Robert Castelo
★ 3.0k • written 14 months ago by
Davide
• 0
1
vote
1
reply
555
views
Cleaning GeneSets from GSEA
msigdb
GSEABase
GSVA
updated 14 months ago by
Robert Castelo
★ 3.0k • written 14 months ago by
forlani.luca
• 0
0
votes
1
reply
418
views
Running PLAGE gets killed
GSVA
SingleCellData
updated 14 months ago by
Robert Castelo
★ 3.0k • written 14 months ago by
Amna
• 0
0
votes
1
reply
715
views
GSVA: for a pathway, can enrichment scores of all samples be negative?
GSVAdata
GSVA
updated 15 months ago by
Robert Castelo
★ 3.0k • written 15 months ago by
random
• 0
0
votes
1
reply
677
views
GSVA package normalization on gene-length ?
GSVA
updated 17 months ago by
Robert Castelo
★ 3.0k • written 17 months ago by
xanthexu
• 0
1
vote
11
replies
1.9k
views
Error in .local(expr, gset.idx.list, ...) : Please install the nnotation package hgu95a, but I can't install hgu95a
GSVA
updated 22 months ago by
soudayo
▴ 10 • written 2.8 years ago by
yaoxucpu
• 0
2
votes
2
replies
1.2k
views
Questions regard to GSVA and Limma
limma
GSVA
23 months ago
Chenxi
• 0
2
votes
2
replies
466
views
Turn of GSVA filtering for method ssGSEA
GSVA
23 months ago
k.vitting.seerup
▴ 120
1
vote
2
replies
941
views
Issue with GSVA using dgCMatrix
GSVA
23 months ago
resa
• 0
0
votes
1
reply
1.8k
views
GSVA Problem
GSVA
updated 2.0 years ago by
Robert Castelo
★ 3.0k • written 2.0 years ago by
tywzlzl2011
• 0
6
votes
4
replies
1.2k
views
Discrepancy in GSVA for Nanostring when using normalized counts vs rlog as input
GSVA
2.3 years ago
hanyin.wang88
▴ 10
0
votes
8
replies
3.7k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 8 months ago by
Robert Castelo
★ 3.0k • written 2.3 years ago by
Siyuan
• 0
2
votes
3
replies
1.3k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 2.4 years ago by
Robert Castelo
★ 3.0k • written 2.4 years ago by
hsiowa2
▴ 20
0
votes
3
replies
878
views
GSVA on gene sets with 2 genes
GSVA
gene sets
RNA-seq
updated 2.6 years ago by
Robert Castelo
★ 3.0k • written 2.6 years ago by
Endre Sebestyén
▴ 60
0
votes
1
reply
700
views
Extract GSVA gene rank matrix
gsva
updated 2.8 years ago by
Robert Castelo
★ 3.0k • written 2.8 years ago by
dylan
• 0
2
votes
1
reply
1.3k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 2.9 years ago by
Robert Castelo
★ 3.0k • written 2.9 years ago by
igor
▴ 40
2
votes
2
replies
1.3k
views
Using GSVA All the pathway score are same
GSVA
scRNA-seq data
updated 2.9 years ago by
Robert Castelo
★ 3.0k • written 2.9 years ago by
initialqy
• 0
2
votes
10
replies
2.5k
views
How to compare two or more GSVA outputs, when it is not possible to run GSVA at once
gsva
updated 2.9 years ago by
Robert Castelo
★ 3.0k • written 2.9 years ago by
hsiowa2
▴ 20
0
votes
1
reply
1.1k
views
GSVA on integrated/batch corrected scRNAseq data
GSVA
Job
updated 3.0 years ago by
Robert Castelo
★ 3.0k • written 3.0 years ago by
laura.derooij
• 0
1
vote
12
replies
1.5k
views
GSVA (running group samples separately)
GSVA
updated 3.1 years ago by
Robert Castelo
★ 3.0k • written 3.1 years ago by
Jenn
▴ 30
7
votes
11
replies
1.5k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 3.1 years ago by
Robert Castelo
★ 3.0k • written 3.1 years ago by
rocanja
▴ 60
0
votes
1
reply
1.1k
views
Method and kcdf arguments in gsva package
GSVA
updated 3.1 years ago by
Robert Castelo
★ 3.0k • written 3.1 years ago by
thkapell
▴ 10
8
votes
6
replies
18k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea
gsva
piano
egsea
updated 2.2 years ago by
calvin99
▴ 10 • written 5.9 years ago by
sina.nassiri
▴ 120
1
vote
4
replies
3.6k
views
GSVA on RNAseq data
gsva
rnaseq
updated 4.2 years ago by
Robert Castelo
★ 3.0k • written 4.2 years ago by
rocanja
▴ 60
0
votes
1
reply
619
views
GSVA lots of positive values, is this expected behavior?
gsva
updated 4.2 years ago by
Robert Castelo
★ 3.0k • written 4.2 years ago by
owen.whitley
▴ 10
1
vote
1
reply
1.1k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
4.9 years ago • updated 4.2 years ago
SB
• 0
5
votes
4
replies
2.1k
views
Differential expression on GSVA scores using LIMMA
limma
gsva
updated 4.2 years ago by
Robert Castelo
★ 3.0k • written 4.2 years ago by
rocanja
▴ 60
2
votes
4
replies
1.7k
views
Are singscore scores comparable between gene sets?
singscore
GSVA
GSEA
subtypes
geneset
updated 2.4 years ago by
bhuva.d
• 0 • written 4.2 years ago by
Pietro
▴ 40
10
votes
10
replies
4.7k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva
gene set variation analysis
normalization
transformation
rna-seq
5.2 years ago • updated 4.4 years ago
rached
▴ 50
0
votes
0
replies
760
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA
geneset
RNASeq
TCGA
subtypes
4.4 years ago
Pietro
▴ 40
1
vote
1
reply
886
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
4.4 years ago
krassowski.michal
▴ 20
2
votes
1
reply
881
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA
tutorial
updated 4.7 years ago by
Robert Castelo
★ 3.0k • written 4.7 years ago by
owen.whitley
▴ 10
1
vote
4
replies
1.4k
views
Meaning of zero for ssGESA value calculated by GSVA package
gsva
updated 4.9 years ago by
Robert Castelo
★ 3.0k • written 4.9 years ago by
Shi-Xiang Wang
• 0
2
votes
2
replies
1.3k
views
Input genes for GSVA
gsva
gene expression matrix
updated 5.1 years ago by
Robert Castelo
★ 3.0k • written 5.1 years ago by
CodeAway
▴ 70
0
votes
4
replies
964
views
The selection of bandwidth of GSVA
GSVA
gsva
updated 5.2 years ago by
Robert Castelo
★ 3.0k • written 5.2 years ago by
Xingyu
• 0
1
vote
2
replies
1.7k
views
GSVA for single sample
gsea
gsva
ssgsea
5.3 years ago
jaison75
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Answer: DESeq2 + analysis question for design with uneven time point design
by
Michael Love
40k
I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…
Answer: Genes with highest differential expression have very low read counts for most ge
by
Michael Love
40k
Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat
by
Gordon Smyth
47k
> equivqalent in limma would be like a gene by gene specificic design matrix where no BL time point would exist but a continuous variable t…
Comment: Extract Limma Adjusted Values for Plotting
by
ATpoint
★ 2.9k
Yes, with normalized counts on log2 scale.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat
by
Anna
▴ 20
A no I never referred to transcriptomic data when I was talking about "standard procedure" I was referring to the way we analyze longitudin…
Votes
A: Ranges from a fasta file
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Awards
• All
Scholar
to
Mike Smith
★ 6.0k
Popular Question
to
Martin Morgan
25k
Teacher
to
deeenes
▴ 30
Popular Question
to
Hervé Pagès
16k
Popular Question
to
Gordon Smyth
47k
Locations
• All
WEHI, Melbourne, Australia,
21 minutes ago
United States,
1 hour ago
United States,
2 hours ago
United States,
2 hours ago
Russia,
2 hours ago
Traffic: 157 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