Showing : ClusterProfiler • reset
2
votes
2
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352
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 15 days ago by ★ 1.2k • written 22 days ago by • 0
7
votes
9
replies
1.1k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 8 weeks ago by ★ 4.1k • written 8 weeks ago by • 0
0
votes
5
replies
596
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 7 weeks ago by ▴ 760 • written 9 weeks ago by • 0
1
vote
2
replies
828
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 10 weeks ago by • 0
0
votes
1
reply
433
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 10 weeks ago by ★ 4.1k • written 10 weeks ago by • 0
1
vote
5
replies
910
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 12 weeks ago by • 0
2
votes
4
replies
750
views
# Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.
clusterProfiler makeOrgPackage gseGO
updated 11 weeks ago by 67k • written 12 weeks ago by • 0
1
vote
2
replies
351
views
Question on number of genes used in GO analysis
GO clusterProfiler
3 months ago Danté • 0
1
vote
1
reply
438
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis clusterProfiler viewPathway gsePathway
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
3
votes
1
reply
824
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 4 months ago by ★ 4.1k • written 4 months ago by ▴ 10
1
vote
2
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644
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
5 months ago sawa • 0
1
vote
9
replies
1.3k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 5 months ago by 67k • written 5 months ago by ▴ 10
0
votes
1
reply
379
views
How can I get gseGO to return all GO terms tested?
clusterProfiler clusterp
updated 5 months ago by 67k • written 5 months ago by • 0
8
votes
6
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5.8k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 5 months ago by ▴ 30 • written 5.5 years ago by ▴ 160
0
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4
replies
566
views
error running enricher from clusterprofiler
clusterProfiler cluster
6 months ago Yael • 0
0
votes
1
reply
657
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 6 months ago by ★ 4.1k • written 6 months ago by • 0
1
vote
1
reply
352
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 6 months ago by 67k • written 6 months ago by ▴ 30
5
votes
13
replies
1.9k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
6 months ago fernanda.backsouza ▴ 30
2
votes
2
replies
714
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 6 months ago by 67k • written 7 months ago by • 0
1
vote
2
replies
955
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
7 months ago Ana • 0
2
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3
replies
760
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
updated 2 days ago by • 0 • written 7 months ago by • 0
0
votes
1
reply
1.1k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
0
votes
1
reply
371
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 7 months ago by 67k • written 7 months ago by • 0
0
votes
0
replies
396
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
7 months ago andromeda • 0
2
votes
2
replies
717
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 7 months ago by ▴ 10
4
votes
4
replies
4.3k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 7 months ago by • 0 • written 6.9 years ago by ▴ 20
2
votes
2
replies
801
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
8 months ago Eva ▴ 10
1
vote
8
replies
4.0k
views
enrichGOgradient color change
clusterProfiler
updated 5 months ago by • 0 • written 12 months ago by • 0
1
vote
1
reply
391
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 9 months ago by 67k • written 9 months ago by • 0
2
votes
15
replies
1.3k
views
Problems with enrichGO
clusterProfiler enrichGO
updated 9 months ago by 42k • written 9 months ago by • 0
0
votes
3
replies
933
views
Unable to install clusterProfiler
clusterProfiler
updated 9 months ago by • 0 • written 9 months ago by • 0
0
votes
2
replies
767
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
9 months ago mello-vieira • 0
0
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1
reply
712
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 9 months ago by 67k • written 9 months ago by • 0
4
votes
2
replies
765
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
0
votes
3
replies
1.6k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
3
votes
6
replies
3.0k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 11 months ago by 67k • written 2.1 years ago by ▴ 10
0
votes
9
replies
1.2k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
11 months ago nromerov • 0
2
votes
9
replies
2.9k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 12 months ago by ▴ 50 • written 12 months ago by ▴ 30
3
votes
4
replies
1.8k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
0
votes
2
replies
761
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
13 months ago georgii.vdovin • 0
0
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0
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588
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
13 months ago nromerov • 0
0
votes
2
replies
1.3k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 13 months ago by 67k • written 13 months ago by • 0
1
vote
2
replies
1.4k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
14 months ago fluentin44 • 0
0
votes
2
replies
2.1k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
14 months ago Valéria • 0
3
votes
2
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1.8k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 15 months ago by ★ 4.1k • written 15 months ago by ▴ 10
0
votes
3
replies
2.1k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 12 months ago by • 0 • written 15 months ago by • 0
0
votes
3
replies
2.3k
views
Not able to install clusterProfiler
clusterProfiler
updated 9 months ago by • 0 • written 16 months ago by • 0
0
votes
0
replies
516
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
16 months ago georgii.vdovin • 0
2
votes
5
replies
3.7k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.8 years ago by • 0
0
votes
1
reply
1.4k
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO GeneSet clusterProfiler GeneSetEnrichment
updated 16 months ago by 67k • written 16 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Comment: Merge Replicates vs Mixed Model by abadgerw • 0
@gabrielhoffman any insight?
Comment: makeContrastsDream for Interaction by abadgerw • 0
@gabrielhoffman any insight?
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta by Michael Love 42k
That is the rows that did converge.
Answer: Is my time course analysis with DESeq2 valid? by Michael Love 42k
For choosing the correct statistical design, I recommend working with a local statistician or someone familiar with linear models in R. I h…
Votes
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
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