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
5
replies
442
views
Identifying potentially associated gene set to drug response using GSVA
drug
RNASeq
GSVA
written 8 weeks ago by
Kent
• 0
1
vote
2
replies
470
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
4 weeks ago
georgii.vdovin
• 0
1
vote
4
replies
986
views
GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment
GSVA
ssGSEA
updated 11 weeks ago by
Tyler Sagendorf
▴ 10 • written 3 months ago by
Bob
▴ 10
4
votes
4
replies
2.5k
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 3 months ago by
Ginny
• 0 • written 13 months ago by
snijesh
▴ 200
0
votes
1
reply
1.2k
views
Job:
Research software engineer at UPF Barcelona
JobPosting
Devel
GSVA
Software
written 2.1 years ago by
Robert Castelo
★ 3.4k
0
votes
1
reply
542
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
1.5k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA
GSVAdata
RNAseq
6 months ago • updated 5 months ago
Lucy
▴ 60
1
vote
1
reply
493
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
509
views
Interpretation of GSVA with absRanking=TRUE
GSVA
7 months ago
gad.abraham
• 0
0
votes
3
replies
1.0k
views
GSVA function
DESeq2
GSVA
ssGSEA
updated 7 months ago by
Robert Castelo
★ 3.4k • written 7 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
369
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
8 months ago
Chris
▴ 20
1
vote
2
replies
4.0k
views
GSVA error
GSVA
9 months ago
Alex
• 0
1
vote
6
replies
974
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
2
votes
7
replies
3.2k
views
Issue with GSVA using dgCMatrix
GSVA
updated 10 months ago by
Moritz
▴ 10 • written 3.6 years ago by
resa
• 0
9
votes
7
replies
21k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea
gsva
piano
egsea
updated 13 months ago by
amin8w
▴ 10 • written 7.5 years ago by
sina.nassiri
▴ 130
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 13 months ago by
arina
• 0 • written 23 months ago by
Omer
• 0
0
votes
1
reply
669
views
GSVA exceeds 1
GSVA
updated 16 months ago by
Robert Castelo
★ 3.4k • written 16 months ago by
Heba
• 0
4
votes
2
replies
2.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 18 months ago by
Gordon Smyth
52k • written 18 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
21 months ago
arashdeep singh
• 0
2
votes
4
replies
2.0k
views
Failed to install Biobase
GSVA
Biobase
updated 21 months ago by
James W. MacDonald
67k • written 21 months ago by
johann.brisseau
• 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 23 months ago by
sharvari gujja
▴ 40
0
votes
3
replies
1.9k
views
GSVA results interpretation
GSVA
updated 2.0 years ago by
Robert Castelo
★ 3.4k • written 2.0 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
2.0 years ago
Zhijie
• 0
1
vote
5
replies
2.1k
views
'combined score' calculation with singscore vs gsva
singscore
GSVA
2.2 years ago
rocanja
▴ 60
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 2.5 years ago by
João
• 0
0
votes
8
replies
7.5k
views
GSVA Error in .mapGeneSetsToFeatures(mapped.gset.idx.list, rownames(expr))
GSVA
updated 2.3 years ago by
Robert Castelo
★ 3.4k • written 3.9 years ago by
Siyuan
• 0
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
2.5 years ago
Yang Shi
▴ 10
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 2.6 years ago
Guandong Shang
▴ 40
2
votes
2
replies
2.0k
views
How to run GSVA with partially NA genes
GSVA
2.6 years ago
blakebowen
• 0
1
vote
3
replies
8.0k
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
1.8k
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 2.8 years ago by
Robert Castelo
★ 3.4k • written 2.8 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 2.8 years ago by
Robert Castelo
★ 3.4k • written 2.8 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
3.5 years ago
Chenxi
• 0
2
votes
2
replies
1.1k
views
Turn of GSVA filtering for method ssGSEA
GSVA
3.5 years ago
k.vitting.seerup
▴ 120
0
votes
1
reply
4.0k
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
3.9 years ago
hanyin.wang88
▴ 10
2
votes
4
replies
3.0k
views
Are singscore scores comparable between gene sets?
singscore
GSVA
GSEA
subtypes
geneset
updated 4.0 years ago by
Dharmesh D Bhuva
• 0 • written 5.8 years ago by
Pietro
▴ 40
2
votes
3
replies
2.4k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 4.0 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 4.2 years ago by
Robert Castelo
★ 3.4k • written 4.3 years ago by
Endre Sebestyén
▴ 70
0
votes
1
reply
1.4k
views
Extract GSVA gene rank matrix
gsva
updated 4.4 years ago by
Robert Castelo
★ 3.4k • written 4.4 years ago by
dylan
• 0
2
votes
1
reply
2.7k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 4.5 years ago by
Robert Castelo
★ 3.4k • written 4.5 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
1.8k
views
GSVA on integrated/batch corrected scRNAseq data
GSVA
Job
updated 4.6 years ago by
Robert Castelo
★ 3.4k • written 4.6 years ago by
laura.derooij
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
by
James W. MacDonald
67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue
by
k.panov
• 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package
by
Lukas
▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts
by
sindhuri
• 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package
by
James W. MacDonald
67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
A: Linear regression in DESeq2
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
Awards
• All
Popular Question
to
Gordon Smyth
52k
Popular Question
to
linouhao
▴ 20
Popular Question
to
spg
• 0
Popular Question
to
otieno43
• 0
Popular Question
to
svlachavas
▴ 840
Locations
• All
United States,
18 minutes ago
Germany/Heidelberg/German Cancer Research Center,
21 minutes ago
UPF, Barcelona, Spain,
25 minutes ago
Kazakhstan,
31 minutes ago
WEHI, Melbourne, Australia,
41 minutes ago
Traffic: 790 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