Showing : clusterprofiler • reset
3
votes
4
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5.2k
views
Analysis of clusters of a heatmap with enrichGO of clusterProfiler: choice fo the categories to visualize
clusterProfiler enrichGO ComplexHeatmap
updated 5 months ago by 68k • written 5 months ago by ▴ 10
1
vote
3
replies
1.3k
views
CluserProfiler message "No gene can be mapped"
clusterProfiler
updated 7 months ago by 68k • written 7 months ago by • 0
0
votes
3
replies
1.3k
views
Gene Ontology (GO) Analysis
GOstats hyperGTest GO enrichGO clusterProfiler
7 months ago GA ▴ 10
0
votes
1
reply
624
views
Error in cnetplot
enrichplot clusterProfiler
updated 8 months ago by ★ 4.1k • written 9 months ago by • 0
0
votes
1
reply
761
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
10 months ago Jessica • 0
0
votes
4
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975
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
10 months ago Quang NN ▴ 10
2
votes
2
replies
914
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 13 months ago by ★ 1.2k • written 13 months ago by • 0
7
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9
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2.0k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
0
votes
5
replies
1.6k
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 14 months ago by ▴ 760 • written 15 months ago by • 0
1
vote
2
replies
3.1k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 15 months ago by • 0
0
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1
reply
1.4k
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
1
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5
replies
2.3k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 16 months ago by • 0
2
votes
4
replies
1.6k
views
# Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.
clusterProfiler makeOrgPackage gseGO
updated 15 months ago by 68k • written 16 months ago by • 0
1
vote
2
replies
876
views
Question on number of genes used in GO analysis
GO clusterProfiler
16 months ago Danté • 0
1
vote
1
reply
1.4k
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis clusterProfiler viewPathway gsePathway
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
3
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1
reply
2.1k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 17 months ago by ★ 4.1k • written 17 months ago by ▴ 10
1
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2
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1.2k
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
18 months ago sawa • 0
1
vote
9
replies
3.3k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 18 months ago by 68k • written 18 months ago by ▴ 10
0
votes
1
reply
881
views
How can I get gseGO to return all GO terms tested?
clusterProfiler clusterp
updated 18 months ago by 68k • written 18 months ago by • 0
8
votes
6
replies
8.8k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 19 months ago by ▴ 30 • written 6.6 years ago by ▴ 180
0
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4
replies
1.5k
views
error running enricher from clusterprofiler
clusterProfiler cluster
19 months ago Yael • 0
0
votes
1
reply
1.4k
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 19 months ago by ★ 4.1k • written 19 months ago by • 0
1
vote
1
reply
767
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 20 months ago by 68k • written 20 months ago by ▴ 30
5
votes
13
replies
4.1k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
20 months ago • updated 19 months ago fernanda.backsouza ▴ 30
2
votes
2
replies
1.6k
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 20 months ago by 68k • written 20 months ago by • 0
1
vote
2
replies
2.6k
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
20 months ago Ana • 0
2
votes
4
replies
2.3k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 20 months ago by • 0
0
votes
2
replies
2.8k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 3 months ago by • 0 • written 20 months ago by • 0
0
votes
1
reply
624
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 20 months ago by 68k • written 20 months ago by • 0
0
votes
0
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729
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
20 months ago andromeda • 0
2
votes
2
replies
1.4k
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 21 months ago by ▴ 10
4
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4
replies
5.3k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 21 months ago by • 0 • written 8.0 years ago by ▴ 20
2
votes
2
replies
1.8k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
21 months ago Eva ▴ 10
3
votes
9
replies
8.2k
views
enrichGOgradient color change
clusterProfiler
updated 11 months ago by • 0 • written 2.1 years ago by • 0
1
vote
1
reply
722
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 22 months ago by 68k • written 22 months ago by • 0
2
votes
15
replies
2.7k
views
Problems with enrichGO
clusterProfiler enrichGO
updated 22 months ago by 43k • written 22 months ago by • 0
0
votes
3
replies
1.6k
views
Unable to install clusterProfiler
clusterProfiler
updated 22 months ago by • 0 • written 22 months ago by • 0
0
votes
2
replies
1.4k
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
22 months ago mello-vieira • 0
0
votes
1
reply
1.4k
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 23 months ago by 68k • written 23 months ago by • 0
4
votes
2
replies
1.4k
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 23 months ago by ★ 4.1k • written 23 months ago by • 0
0
votes
3
replies
2.6k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 2.0 years ago by ★ 4.1k • written 2.0 years ago by • 0
3
votes
6
replies
4.4k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 2.0 years ago by 68k • written 3.1 years ago by ▴ 10
0
votes
9
replies
2.2k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
2.1 years ago • updated 2.0 years ago nromerov • 0
2
votes
9
replies
3.6k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 2.1 years ago by ▴ 50 • written 2.1 years ago by ▴ 30
3
votes
4
replies
2.9k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 2.1 years ago by ★ 4.1k • written 2.1 years ago by • 0
0
votes
2
replies
1.1k
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
2.2 years ago georgii.vdovin • 0
0
votes
0
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885
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
2.2 years ago nromerov • 0
0
votes
2
replies
2.3k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
1
vote
2
replies
2.2k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
2.3 years ago fluentin44 • 0
0
votes
2
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3.5k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
2.3 years ago Valéria • 0
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Comment: Bioinformatician at the Lausanne University Hospital by eja.ger.m • 0
For individuals looking to improve communication and collaboration in demanding medical or research environments like the Genetic Medicine …
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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