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Showing :
Gsea
•
reset
0
votes
4
replies
376
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2
GSEA
clusterProfiler
9 days ago • updated 7 days 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 3 months ago by
James W. MacDonald
67k • written 3 months ago by
Gordon
• 0
1
vote
2
replies
1.4k
views
How to use compareCluster in ClusterProfiler?
RNASeqData
GSEA
clusterProfiler
written 4 months ago by
b8177
• 0
0
votes
1
reply
583
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
866
views
Error in gseDO function
DOSE
gsea
8 months ago
Javier
• 0
0
votes
2
replies
1.2k
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
10 months ago
Gordon
• 0
2
votes
2
replies
873
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
written 10 months ago by
enee
▴ 10
4
votes
3
replies
768
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 10 months ago by
Georg
• 0
0
votes
1
reply
1.5k
views
choosing rank for GSEA
gsea
DESeq2
updated 15 months ago by
ATpoint
★ 4.6k • written 15 months ago by
Grace.Ciabattoni
• 0
0
votes
3
replies
2.4k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot
GSEA
clusterProfiler
updated 15 months ago by
Fatemeh
• 0 • written 17 months ago by
Cen
• 0
0
votes
0
replies
950
views
using fgsea to compare two datasets
GSEA
fgsea
18 months ago
Cen
• 0
1
vote
1
reply
1.6k
views
How to do GSEA over limma + voom DGE ?
GSEA
voom
limma
updated 18 months ago by
Gordon Smyth
52k • written 18 months ago by
manuelsokolov
• 0
8
votes
8
replies
14k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 21 months ago by
ATpoint
★ 4.6k • written 8.5 years ago by
EJ
▴ 20
2
votes
3
replies
1.5k
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
808
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 2.1 years ago by
Guido Hooiveld
★ 4.1k • written 2.1 years ago by
Lawrence
• 0
7
votes
6
replies
3.4k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 2.1 years ago by
Gordon Smyth
52k • written 2.1 years ago by
nhaus
▴ 70
2
votes
3
replies
1.3k
views
system.file() failed to load .gmt file.
pathwayPCA
Gsea
updated 2.2 years ago by
gabriel.odom
• 0 • written 2.2 years ago by
Mikołaj Mierzejewski
• 0
2
votes
4
replies
1.7k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 2.5 years ago by
Gordon Smyth
52k • written 2.5 years ago by
Yang Shi
▴ 10
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 2.6 years ago by
João
• 0
0
votes
2
replies
5.0k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
2.6 years ago
Bhavana
• 0
0
votes
1
reply
1.8k
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
10k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 11 months ago by
ATpoint
★ 4.6k • 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
3.4k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler
KEGG
GSEA
4.0 years ago
Emilia
▴ 40
0
votes
1
reply
1.0k
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO
GSEA
4.2 years ago
lessismore
▴ 20
2
votes
1
reply
2.8k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 4.5 years ago by
Robert Castelo
★ 3.4k • written 4.6 years ago by
igor
▴ 50
7
votes
11
replies
3.2k
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
4.2k
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 5.7 years ago by
Gordon Smyth
52k • written 5.7 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 5.9 years ago by
Pietro
▴ 40
0
votes
1
reply
1.0k
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA
Qusage
5.9 years ago
Diana
▴ 10
0
votes
1
reply
3.4k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
5.9 years ago
aboumarshal
• 0
3
votes
7
replies
29k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2
gsea
rnaseq
gene espression
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
bmreilly
• 0
3
votes
3
replies
2.1k
views
Enrichment Analysis with only GeneSymbols
R
GSEA
rna-seq
scRna-Seq
updated 5.9 years ago by
Peter Langfelder
★ 3.0k • written 5.9 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 6.2 years ago by
abelsousa
• 0
0
votes
2
replies
1.7k
views
GSEA using TFs as the gene set
GSEA
transcription factor binding site enrichment analysis
updated 6.2 years ago by
lhuang7
▴ 50 • written 6.2 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 6.3 years ago by
Gordon Smyth
52k • written 6.3 years ago by
Bogdan
▴ 670
0
votes
2
replies
1.5k
views
Warning in bayes fit in MAST GSEA
MAST
GSEA
bayesglm.fit
6.4 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
1.2k
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
6.5 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 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
csijst
• 0
1
vote
2
replies
2.1k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
6.6 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
4.8k
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 7.0 years ago by
Guangchuang Yu
★ 1.2k • written 7.0 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
Recent ...
Replies
Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot
by
Quang NN
▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Prakash Sah
• 0
Thanks James!
Votes
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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