Showing : GSEA • reset
2
votes
1
reply
140
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3 months ago by 3.1k • written 3 months ago by • 0
0
votes
2
replies
236
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler KEGG GSEA
4 months ago Emilia ▴ 30
0
votes
1
reply
115
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
6 months ago lessismore • 0
2
votes
1
reply
258
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 11 months ago by ★ 2.7k • written 11 months ago by ▴ 40
7
votes
11
replies
464
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 13 months ago by ★ 2.7k • written 13 months ago by ▴ 60
0
votes
2
replies
562
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 23 months ago by ▴ 50 • written 24 months ago by • 0
3
votes
5
replies
717
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 90
2
votes
4
replies
605
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 5 months ago by • 0 • written 2.3 years ago by ▴ 30
0
votes
1
reply
250
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
2.3 years ago Diana ▴ 10
0
votes
1
reply
306
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
2.3 years ago aboumarshal • 0
3
votes
7
replies
2.5k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 2.3 years ago by 33k • written 2.3 years ago by • 0
3
votes
3
replies
439
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 2.3 years ago by ★ 2.6k • written 2.3 years ago by ▴ 50
0
votes
3
replies
585
views
gseaplot vertical line
clusterProfiler gsea
updated 2.5 years ago by 0 • written 2.6 years ago by • 0
0
votes
2
replies
397
views
GSEA using TFs as the gene set
GSEA transcription factor binding site enrichment analysis
updated 2.6 years ago by ▴ 50 • written 2.6 years ago by ▴ 10
0
votes
1
reply
458
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2 gsea tpm rnaseq salmon rna seq
updated 2.7 years ago by 33k • written 2.7 years ago by • 0
0
votes
2
replies
480
views
gene set enrichment analysis
GSEA GSA
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 610
0
votes
2
replies
441
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
2.8 years ago santos22903 • 0
2
votes
7
replies
672
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
0
replies
409
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
2.9 years ago l.brown ▴ 10
0
votes
3
replies
810
views
fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
2.9 years ago atakanekiz ▴ 30
0
votes
3
replies
653
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 3.0 years ago by 33k • written 3.0 years ago by • 0
1
vote
2
replies
780
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
3.0 years ago martin.busch • 0
1
vote
1
reply
576
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea rattus norvegicus
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 10
2
votes
2
replies
1.2k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 3.3 years ago by ★ 1.2k • written 3.3 years ago by • 0
1
vote
2
replies
767
views
GSVA for single sample
gsea gsva ssgsea
3.4 years ago jaison75 ▴ 20
0
votes
2
replies
552
views
merging gseaResult objects
clusterprofiler gsea
updated 3.4 years ago by ★ 1.2k • written 3.4 years ago by • 0
1
vote
1
reply
552
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
3.4 years ago Stane ▴ 40
0
votes
0
replies
623
views
GSEA-class file (.cls) parsing error message
gsea
3.5 years ago snguyen268 • 0
0
votes
1
reply
1.1k
views
gseaplot() function of clusterProfiler went wrong
gsea clusterprofiler
3.6 years ago giuseppe0525 • 0
2
votes
6
replies
3.9k
views
GSEA using clusterProfiler
GSEA clusterProfiler
3.6 years ago giuseppe0525 • 0
4
votes
1
reply
939
views
GSEA using clusterprofileR
clusterprofiler gsea
updated 3.7 years ago by ▴ 200 • written 3.7 years ago by ▴ 30
0
votes
1
reply
468
views
BioQC R package issue with broad gmt files
R BioQC gmt GSEA
3.7 years ago Seymoo • 0
0
votes
2
replies
676
views
Resolved- GSEAbase: goSlim function, pb with counts
GSEA GO goSlim
3.8 years ago maeva.mollion • 0
1
vote
1
reply
565
views
two-color microarray - Gene Set Enrichment Analysis
Twocolor microarray GSEA
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
2
votes
3
replies
1.1k
views
custom annotation for GO enrichment
annotationforge GSEA clusterprofiler GO annotation
3.9 years ago cabezasdelafuented ▴ 10
2
votes
1
reply
2.1k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST scRNA GSEA
updated 3.9 years ago by ▴ 260 • written 3.9 years ago by • 0
1
vote
5
replies
1.0k
views
FGSEA only runs with <1000 permutations
fgsea gsea
updated 3.9 years ago by ▴ 200 • written 3.9 years ago by • 0
0
votes
1
reply
725
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
4.0 years ago bhgyu ▴ 30
0
votes
1
reply
1.0k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 4.1 years ago by ★ 1.5k • written 4.1 years ago by • 0
1
vote
1
reply
640
views
Python Module from Kim and Volsky (2005) PAGE: Parametric Analysis of Gene Set Enrichment paper?
GSEA PAGE microarray differential gene expression pathway analysis
updated 4.2 years ago by ★ 3.0k • written 4.2 years ago by • 0
0
votes
3
replies
1.1k
views
topGO - treating up- and down-regulated genes separately
topGO GSEA pathway analysis
updated 4.3 years ago by ▴ 640 • written 4.3 years ago by • 0
1
vote
2
replies
1.2k
views
how to perform pre ranked GSEA in R?
r microarray statistics GSEA
updated 4.3 years ago by • 0 • written 6.3 years ago by ▴ 80
2
votes
3
replies
847
views
EGSEA usage with microarray data (with vooma)?
EGSEA gene set testing vooma limma voom gsea
4.5 years ago • updated 4.4 years ago Pekka Kohonen ▴ 190
0
votes
7
replies
1.1k
views
Statistic for GSA
gsea concept gsa
updated 4.4 years ago by ▴ 190 • written 4.4 years ago by ▴ 640
2
votes
1
reply
776
views
Direction aware fgsea test
fgsea gsea
updated 4.4 years ago by ▴ 200 • written 4.4 years ago by ▴ 90
1
vote
4
replies
1.0k
views
GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 4.6 years ago by ★ 1.2k • written 4.8 years ago by ▴ 90
0
votes
4
replies
914
views
EGSEA: how does the program generate the value for the up or down regulation of gene sets or pathways
pathways gsea egsea gage
updated 4.7 years ago by ▴ 40 • written 4.7 years ago by • 0
0
votes
1
reply
1.1k
views
ClusterProfiler can't load gmt file
GSEA clusterprofiler gmt
updated 4.8 years ago by ★ 1.2k • written 4.8 years ago by • 0
3
votes
1
reply
5.0k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 4.9 years ago by 33k • written 4.9 years ago by ▴ 10
9
votes
6
replies
3.3k
views
GSEA-like enrichment score calculation
GSEA enrichment analysis gseabase
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: Annotation using QSEA package by rtrivedi1 ▴ 10
Issue is fixed now !! Thanks Rakesh
Comment: Binding matrix created by DiffBind by sh.kazempour94 ▴ 10
Thank you for helping me figuring this out! The matrix from dba.peakset() seems to be the correct one. Thanks!
Comment: Annotation using QSEA package by James W. MacDonald 57k
OK. This is the part I meant about using an accessor. There is a function called `genome` that does what you have tried to do. It actually …
Comment: Annotation using QSEA package by rtrivedi1 ▴ 10
Hi, Step 1: I used the following code to get hg38_anno_final: ``` library(annotatr) library(TxDb.Hsapiens.UCSC.hg38.knownGene) hg38_ann…
Comment: Annotation using QSEA package by rtrivedi1 ▴ 10
I used the following code to get hg38_anno_final: ``` library(annotatr) library(TxDb.Hsapiens.UCSC.hg38.knownGene) hg38_annot <- builtin…
Votes
Comment: Annotation using QSEA package
Comment: Binding matrix created by DiffBind
Comment: Annotation using QSEA package
Answer: Annotation using QSEA package
Answer: lmFit, number of proteins
Awards • All
Scholar to Gordon Smyth 43k
Scholar to Robert Castelo ★ 2.7k
Scholar to Michael Love 33k
Scholar to James W. MacDonald 57k
Scholar to Martin Morgan 25k
Locations • All
United States, 2 minutes ago
Naas, Republic of Ireland, 15 minutes ago
United States, 1 hour ago
United States, 1 hour ago
Australia, 1 hour ago
Traffic: 261 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