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GSEa
•
reset
0
votes
4
replies
457
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2
GSEA
clusterProfiler
4 weeks ago
Quang NN
▴ 10
1
vote
8
replies
1.1k
views
Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
gsea
mice
org.Mm.eg.db
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
Gordon
• 0
1
vote
2
replies
1.7k
views
How to use compareCluster in ClusterProfiler?
RNASeqData
GSEA
clusterProfiler
written 5 months ago by
b8177
• 0
0
votes
1
reply
625
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea
GSVA
gsea
updated 6 months ago by
Axel Klenk
★ 1.1k • written 6 months ago by
Bioinformagician
• 0
1
vote
4
replies
940
views
Error in gseDO function
DOSE
gsea
9 months ago • updated 8 months ago
Javier
• 0
0
votes
2
replies
1.3k
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
11 months ago • updated 10 months ago
Gordon
• 0
2
votes
2
replies
954
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
written 11 months ago by
enee
▴ 10
4
votes
3
replies
821
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 11 months ago by
Georg
• 0
0
votes
1
reply
1.7k
views
choosing rank for GSEA
gsea
DESeq2
updated 16 months ago by
ATpoint
★ 4.7k • written 16 months ago by
Grace.Ciabattoni
• 0
0
votes
3
replies
2.5k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot
GSEA
clusterProfiler
updated 16 months ago by
Fatemeh
• 0 • written 18 months ago by
Cen
• 0
0
votes
0
replies
987
views
using fgsea to compare two datasets
GSEA
fgsea
19 months ago
Cen
• 0
1
vote
1
reply
1.7k
views
How to do GSEA over limma + voom DGE ?
GSEA
voom
limma
updated 19 months ago by
Gordon Smyth
52k • written 19 months ago by
manuelsokolov
• 0
8
votes
8
replies
14k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 22 months ago by
ATpoint
★ 4.7k • written 8.6 years ago by
EJ
▴ 20
2
votes
3
replies
1.6k
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 2.1 years ago by
belinda.phipson
▴ 40 • written 2.1 years ago by
Lukas
• 0
0
votes
1
reply
829
views
GSA type of input data
GSEA
GSA
vst
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
nhaus
▴ 70
0
votes
1
reply
1.3k
views
DGE genes are not available in GSEA
dge
gsea
updated 2.2 years ago by
Guido Hooiveld
★ 4.1k • written 2.2 years ago by
Lawrence
• 0
7
votes
6
replies
3.6k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 2.1 years ago by
Gordon Smyth
52k • written 2.2 years ago by
nhaus
▴ 70
2
votes
3
replies
1.3k
views
system.file() failed to load .gmt file.
pathwayPCA
Gsea
updated 2.3 years ago by
gabriel.odom
• 0 • written 2.3 years ago by
Mikołaj Mierzejewski
• 0
2
votes
4
replies
1.7k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 2.6 years ago by
Gordon Smyth
52k • written 2.6 years ago by
Yang Shi
▴ 10
0
votes
3
replies
3.1k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA
GSVA
updated 2.3 years ago by
rocanja
▴ 60 • written 2.6 years ago by
João
• 0
0
votes
2
replies
5.2k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
2.7 years ago • updated 2.6 years ago
Bhavana
• 0
0
votes
1
reply
1.9k
views
GSEA using custom GO annotations
RNASeq
GSEA
updated 2.9 years ago by
Robert Castelo
★ 3.4k • written 2.9 years ago by
jms2520
▴ 10
12
votes
13
replies
11k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 12 months ago by
ATpoint
★ 4.7k • written 2.9 years ago by
nhaus
▴ 70
2
votes
1
reply
1.2k
views
GSEA generate genesets
pathway
KEGGREST
GSEA
updated 3.9 years ago by
Kevin Blighe
★ 4.0k • written 3.9 years ago by
MOHAMMAD
• 0
0
votes
2
replies
3.5k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler
KEGG
GSEA
4.1 years ago • updated 4.0 years ago
Emilia
▴ 40
0
votes
1
reply
1.1k
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO
GSEA
4.2 years ago
lessismore
▴ 20
2
votes
1
reply
2.9k
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
7
votes
11
replies
3.3k
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
2
votes
2
replies
4.3k
views
ClusterProfiler GSEA with geneList
clusterProfiler
GSEA
geneList
updated 5.6 years ago by
Ludwig Geistlinger
▴ 70 • written 5.6 years ago by
lucap
• 0
8
votes
5
replies
4.4k
views
How to get t-statistic values using edgeR?
r
edger
t-statistic
fgsea
gsea
updated 5.8 years ago by
Gordon Smyth
52k • written 5.8 years ago by
Biologist
▴ 120
2
votes
4
replies
3.1k
views
Are singscore scores comparable between gene sets?
singscore
GSVA
GSEA
subtypes
geneset
updated 4.1 years ago by
Dharmesh D Bhuva
• 0 • written 6.0 years ago by
Pietro
▴ 40
0
votes
1
reply
1.1k
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA
Qusage
6.0 years ago • updated 5.9 years ago
Diana
▴ 10
0
votes
1
reply
3.5k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
6.0 years ago
aboumarshal
• 0
3
votes
7
replies
29k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2
gsea
rnaseq
gene espression
updated 6.0 years ago by
Michael Love
43k • written 6.0 years ago by
bmreilly
• 0
3
votes
3
replies
2.2k
views
Enrichment Analysis with only GeneSymbols
R
GSEA
rna-seq
scRna-Seq
updated 6.0 years ago by
Peter Langfelder
★ 3.0k • written 6.0 years ago by
hamza_karakurt
▴ 60
0
votes
3
replies
1.6k
views
gseaplot vertical line
clusterProfiler
gsea
updated 6.1 years ago by
Bioconductor Community
0 • written 6.3 years ago by
abelsousa
• 0
0
votes
2
replies
1.8k
views
GSEA using TFs as the gene set
GSEA
transcription factor binding site enrichment analysis
updated 6.3 years ago by
lhuang7
▴ 50 • written 6.3 years ago by
thkapell
▴ 10
0
votes
1
reply
1.4k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2
gsea
tpm
rnaseq
salmon rna seq
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
leo_CD
• 0
0
votes
2
replies
2.0k
views
gene set enrichment analysis
GSEA
GSA
updated 6.4 years ago by
Gordon Smyth
52k • written 6.4 years ago by
Bogdan
▴ 670
0
votes
2
replies
1.5k
views
Warning in bayes fit in MAST GSEA
MAST
GSEA
bayesglm.fit
6.5 years ago
santos22903
• 0
5
votes
7
replies
3.6k
views
GSEA for RNA-seq analysis
GSEA
Limma
preranked GSEA
tTest
updated 6.5 years ago by
Gordon Smyth
52k • written 6.5 years ago by
imalumberjack
▴ 10
0
votes
0
replies
1.3k
views
Job:
2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job
rna-seq
chipseq
gsea
python
Job
6.5 years ago
l.brown
▴ 10
0
votes
3
replies
3.7k
views
fgsea p-values are mostly the same upon analysis
fgsea
gsea
sc-rnaseq
6.6 years ago
atakanekiz
▴ 30
0
votes
3
replies
2.1k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA
DESeq2
gseabase
GSEA
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
csijst
• 0
1
vote
2
replies
2.1k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
6.7 years ago
martin.busch
• 0
1
vote
1
reply
1.6k
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea
rattus norvegicus
updated 6.8 years ago by
Gordon Smyth
52k • written 6.8 years ago by
Aurora
▴ 20
2
votes
2
replies
4.9k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler
GSEA
MSIGDB
updated 6.9 years ago by
Guangchuang Yu
★ 1.2k • written 6.9 years ago by
thomasjenner333
• 0
1
vote
2
replies
2.8k
views
GSVA for single sample
gsea
gsva
ssgsea
7.0 years ago
jaison75
▴ 20
0
votes
2
replies
2.1k
views
merging gseaResult objects
clusterprofiler
gsea
updated 7.1 years ago by
Guangchuang Yu
★ 1.2k • written 7.1 years ago by
robmarin
• 0
1
vote
1
reply
2.3k
views
Inconsistency of results GSEA clusterprofiler
gsea
clusterprofiler
7.1 years ago
Stane
▴ 40
50 results • Page
1 of 1
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Replies
Comment: Differential variance analysis - can i use deseq2
by
Michael Love
43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis
by
Gordon Smyth
52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA
by
pammelala304
• 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get()
by
Matthew Thornton
▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data
by
user_bioinfo
• 0
yes actually that's why I did, and its all good! thank you for your response
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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