Showing : clusterProfiler • reset
3
votes
4
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5.6k
views
Analysis of clusters of a heatmap with enrichGO of clusterProfiler: choice fo the categories to visualize
clusterProfiler enrichGO ComplexHeatmap
updated 7 months ago by 68k • written 8 months ago by ▴ 10
1
vote
3
replies
1.4k
views
CluserProfiler message "No gene can be mapped"
clusterProfiler
updated 9 months ago by 68k • written 9 months ago by • 0
0
votes
3
replies
1.5k
views
Gene Ontology (GO) Analysis
GOstats hyperGTest GO enrichGO clusterProfiler
9 months ago GA ▴ 10
0
votes
1
reply
879
views
Error in cnetplot
enrichplot clusterProfiler
updated 10 months ago by ★ 4.1k • written 11 months ago by • 0
0
votes
1
reply
868
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
12 months ago Jessica • 0
0
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4
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1.3k
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
12 months ago Quang NN ▴ 10
2
votes
2
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1.3k
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 15 months ago by ★ 1.2k • written 15 months ago by • 0
7
votes
9
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2.2k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
0
votes
5
replies
1.9k
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 16 months ago by ▴ 760 • written 17 months ago by • 0
1
vote
2
replies
4.0k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 17 months ago by • 0
0
votes
1
reply
1.9k
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
1
vote
5
replies
2.6k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 18 months ago by • 0
2
votes
4
replies
1.9k
views
# Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.
clusterProfiler makeOrgPackage gseGO
updated 17 months ago by 68k • written 18 months ago by • 0
1
vote
2
replies
990
views
Question on number of genes used in GO analysis
GO clusterProfiler
18 months ago Danté • 0
1
vote
1
reply
2.3k
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis clusterProfiler viewPathway gsePathway
updated 19 months ago by ★ 4.1k • written 19 months ago by • 0
3
votes
1
reply
2.6k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 19 months ago by ★ 4.1k • written 19 months ago by ▴ 10
1
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2
replies
1.3k
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
20 months ago sawa • 0
1
vote
9
replies
4.1k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 20 months ago by 68k • written 20 months ago by ▴ 10
0
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1
reply
1.1k
views
How can I get gseGO to return all GO terms tested?
clusterProfiler clusterp
updated 20 months ago by 68k • written 20 months ago by • 0
8
votes
6
replies
11k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 21 months ago by ▴ 30 • written 6.8 years ago by ▴ 180
0
votes
4
replies
1.6k
views
error running enricher from clusterprofiler
clusterProfiler cluster
21 months ago Yael • 0
0
votes
1
reply
2.0k
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 21 months ago by ★ 4.1k • written 21 months ago by • 0
1
vote
1
reply
840
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 22 months ago by 68k • written 22 months ago by ▴ 30
5
votes
13
replies
4.5k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
22 months ago fernanda.backsouza ▴ 30
2
votes
2
replies
1.9k
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 22 months ago by 68k • written 22 months ago by • 0
1
vote
2
replies
3.0k
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
22 months ago Ana • 0
2
votes
4
replies
2.7k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 22 months ago by • 0
0
votes
2
replies
3.3k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 5 months ago by • 0 • written 22 months ago by • 0
0
votes
1
reply
680
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 22 months ago by 68k • written 22 months ago by • 0
0
votes
0
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826
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
22 months ago andromeda • 0
2
votes
2
replies
1.6k
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 23 months ago by ▴ 10
4
votes
4
replies
5.6k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 23 months ago by • 0 • written 8.2 years ago by ▴ 20
2
votes
2
replies
2.0k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
23 months ago Eva ▴ 30
3
votes
9
replies
9.1k
views
enrichGOgradient color change
clusterProfiler
updated 13 months ago by • 0 • written 2.3 years ago by • 0
1
vote
1
reply
783
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 24 months ago by 68k • written 24 months ago by • 0
2
votes
15
replies
2.9k
views
Problems with enrichGO
clusterProfiler enrichGO
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
0
votes
3
replies
1.8k
views
Unable to install clusterProfiler
clusterProfiler
updated 24 months ago by • 0 • written 2.0 years ago by • 0
0
votes
2
replies
1.5k
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
2.0 years ago mello-vieira • 0
0
votes
1
reply
1.6k
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
4
votes
2
replies
1.5k
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 2.1 years ago by ★ 4.1k • written 2.1 years ago by • 0
0
votes
3
replies
2.9k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 2.2 years ago by ★ 4.1k • written 2.2 years ago by • 0
3
votes
6
replies
4.7k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 2.2 years ago by 68k • written 3.3 years ago by ▴ 10
0
votes
9
replies
2.5k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
2.2 years ago nromerov • 0
2
votes
9
replies
3.8k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 2.3 years ago by ▴ 50 • written 2.3 years ago by ▴ 30
3
votes
4
replies
3.1k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 2.3 years ago by ★ 4.1k • written 2.3 years ago by • 0
0
votes
2
replies
1.2k
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
2.3 years ago georgii.vdovin • 0
0
votes
0
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987
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
2.3 years ago nromerov • 0
0
votes
2
replies
2.5k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
1
vote
2
replies
2.4k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
2.4 years ago fluentin44 • 0
0
votes
2
replies
3.9k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
2.5 years ago Valéria • 0
288 results • Page 1 of 6
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Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Votes
Answer: Subsetting data verses contrasts [DESeq2]?
A: WGCNA differences two groups 10 replicates each group
A: WGCNA sample size minimum: why?
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
Answer: Can you colour dendrogram branch clusters in pheatmap?
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