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GSEA
•
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0
votes
2
replies
376
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
8 weeks ago • updated 6 weeks ago
Gordon
• 0
2
votes
1
reply
238
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 8 weeks ago by
Guido Hooiveld
★ 4.0k • written 8 weeks ago by
enee
▴ 10
4
votes
3
replies
265
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 9 weeks ago by
Georg
• 0
0
votes
1
reply
668
views
choosing rank for GSEA
gsea
DESeq2
updated 7 months ago by
ATpoint
★ 4.1k • written 7 months ago by
Grace.Ciabattoni
• 0
0
votes
3
replies
1.4k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot
GSEA
clusterProfiler
updated 7 months ago by
Fatemeh
• 0 • written 9 months ago by
Cen
• 0
0
votes
0
replies
645
views
using fgsea to compare two datasets
GSEA
fgsea
10 months ago
Cen
• 0
1
vote
1
reply
1.0k
views
How to do GSEA over limma + voom DGE ?
GSEA
voom
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
manuelsokolov
• 0
7
votes
8
replies
11k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 13 months ago by
ATpoint
★ 4.1k • written 7.8 years ago by
EJ
▴ 20
2
votes
3
replies
961
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 16 months ago by
belinda.phipson
▴ 40 • written 16 months ago by
Lukas
• 0
0
votes
1
reply
611
views
GSA type of input data
GSEA
GSA
vst
updated 16 months ago by
Michael Love
42k • written 16 months ago by
nhaus
▴ 30
0
votes
1
reply
838
views
DGE genes are not available in GSEA
dge
gsea
updated 17 months ago by
Guido Hooiveld
★ 4.0k • written 17 months ago by
Lawrence
• 0
7
votes
6
replies
2.2k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 16 months ago by
Gordon Smyth
50k • written 17 months ago by
nhaus
▴ 30
2
votes
3
replies
928
views
system.file() failed to load .gmt file.
pathwayPCA
Gsea
updated 18 months ago by
gabriel.odom
• 0 • written 18 months ago by
Mikołaj Mierzejewski
• 0
2
votes
4
replies
1.4k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 22 months ago by
Gordon Smyth
50k • written 22 months ago by
Yang Shi
▴ 10
0
votes
3
replies
2.0k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA
GSVA
updated 18 months ago by
rocanja
▴ 60 • written 22 months ago by
João
• 0
0
votes
2
replies
3.4k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
23 months ago
Bhavana
• 0
0
votes
1
reply
1.1k
views
GSEA using custom GO annotations
RNASeq
GSEA
updated 2.2 years ago by
Robert Castelo
★ 3.3k • written 2.2 years ago by
jms2520
▴ 10
9
votes
13
replies
6.8k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 3 months ago by
ATpoint
★ 4.1k • written 2.2 years ago by
nhaus
▴ 30
2
votes
1
reply
990
views
GSEA generate genesets
pathway
KEGGREST
GSEA
updated 3.2 years ago by
Kevin Blighe
★ 3.9k • written 3.2 years ago by
MOHAMMAD
• 0
0
votes
2
replies
2.3k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler
KEGG
GSEA
3.3 years ago
Emilia
▴ 30
0
votes
1
reply
829
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO
GSEA
3.5 years ago
lessismore
▴ 20
2
votes
1
reply
2.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 3.9 years ago by
Robert Castelo
★ 3.3k • written 3.9 years ago by
igor
▴ 50
7
votes
11
replies
2.5k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 4.1 years ago by
Robert Castelo
★ 3.3k • written 4.1 years ago by
rocanja
▴ 60
2
votes
2
replies
3.2k
views
ClusterProfiler GSEA with geneList
clusterProfiler
GSEA
geneList
updated 4.9 years ago by
Ludwig Geistlinger
▴ 70 • written 4.9 years ago by
lucap
• 0
8
votes
5
replies
3.5k
views
How to get t-statistic values using edgeR?
r
edger
t-statistic
fgsea
gsea
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
Biologist
▴ 110
2
votes
4
replies
2.5k
views
Are singscore scores comparable between gene sets?
singscore
GSVA
GSEA
subtypes
geneset
updated 3.4 years ago by
Dharmesh D Bhuva
• 0 • written 5.2 years ago by
Pietro
▴ 40
0
votes
1
reply
826
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA
Qusage
5.2 years ago
Diana
▴ 10
0
votes
1
reply
2.5k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
5.2 years ago
aboumarshal
• 0
3
votes
7
replies
26k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2
gsea
rnaseq
gene espression
updated 5.2 years ago by
Michael Love
42k • written 5.2 years ago by
bmreilly
• 0
3
votes
3
replies
1.6k
views
Enrichment Analysis with only GeneSymbols
R
GSEA
rna-seq
scRna-Seq
updated 5.2 years ago by
Peter Langfelder
★ 3.0k • written 5.2 years ago by
hamza_karakurt
▴ 50
0
votes
3
replies
1.3k
views
gseaplot vertical line
clusterProfiler
gsea
updated 5.4 years ago by
Bioconductor Community
0 • written 5.5 years ago by
abelsousa
• 0
0
votes
2
replies
1.3k
views
GSEA using TFs as the gene set
GSEA
transcription factor binding site enrichment analysis
updated 5.5 years ago by
lhuang7
▴ 50 • written 5.5 years ago by
thkapell
▴ 10
0
votes
1
reply
1.2k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2
gsea
tpm
rnaseq
salmon rna seq
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
leo_CD
• 0
0
votes
2
replies
1.6k
views
gene set enrichment analysis
GSEA
GSA
updated 5.6 years ago by
Gordon Smyth
50k • written 5.6 years ago by
Bogdan
▴ 670
0
votes
2
replies
1.2k
views
Warning in bayes fit in MAST GSEA
MAST
GSEA
bayesglm.fit
5.7 years ago
santos22903
• 0
5
votes
7
replies
2.6k
views
GSEA for RNA-seq analysis
GSEA
Limma
preranked GSEA
tTest
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
imalumberjack
▴ 10
0
votes
0
replies
1.1k
views
Job:
2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job
rna-seq
chipseq
gsea
python
Job
5.8 years ago
l.brown
▴ 10
0
votes
3
replies
2.9k
views
fgsea p-values are mostly the same upon analysis
fgsea
gsea
sc-rnaseq
5.8 years ago
atakanekiz
▴ 30
0
votes
3
replies
1.8k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA
DESeq2
gseabase
GSEA
updated 5.9 years ago by
Michael Love
42k • written 5.9 years ago by
csijst
• 0
1
vote
2
replies
1.8k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
5.9 years ago
martin.busch
• 0
1
vote
1
reply
1.4k
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea
rattus norvegicus
updated 6.1 years ago by
Gordon Smyth
50k • written 6.1 years ago by
Aurora
▴ 20
2
votes
2
replies
4.1k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler
GSEA
MSIGDB
updated 6.2 years ago by
Guangchuang Yu
★ 1.2k • written 6.2 years ago by
thomasjenner333
• 0
1
vote
2
replies
2.4k
views
GSVA for single sample
gsea
gsva
ssgsea
6.3 years ago
jaison75
▴ 20
0
votes
2
replies
1.7k
views
merging gseaResult objects
clusterprofiler
gsea
updated 6.3 years ago by
Guangchuang Yu
★ 1.2k • written 6.3 years ago by
robmarin
• 0
1
vote
1
reply
1.8k
views
Inconsistency of results GSEA clusterprofiler
gsea
clusterprofiler
6.4 years ago
Stane
▴ 40
0
votes
0
replies
1.3k
views
GSEA-class file (.cls) parsing error message
gsea
6.4 years ago
snguyen268
• 0
0
votes
1
reply
2.4k
views
gseaplot() function of clusterProfiler went wrong
gsea
clusterprofiler
6.5 years ago
giuseppe0525
• 0
2
votes
6
replies
12k
views
GSEA using clusterProfiler
GSEA
clusterProfiler
6.5 years ago
giuseppe0525
• 0
4
votes
1
reply
3.3k
views
GSEA using clusterprofileR
clusterprofiler
gsea
updated 6.6 years ago by
alserg
▴ 260 • written 6.6 years ago by
sup230
▴ 30
0
votes
1
reply
1.1k
views
BioQC R package issue with broad gmt files
R
BioQC
gmt
GSEA
6.6 years ago
Seymoo
• 0
50 results • Page
1 of 1
Recent ...
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Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
by
James W. MacDonald
66k
Yes, you can use `limma`.
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
66k
In that case, probably easiest to subset to the groups being compared.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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