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
615
views
Error in cnetplot
enrichplot clusterProfiler
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
1
reply
756
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
10 months ago Jessica • 0
0
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4
replies
964
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
910
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
votes
9
replies
2.0k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 14 months ago by ★ 4.1k • written 15 months ago by • 0
0
votes
5
replies
1.5k
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
votes
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 15 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 15 months ago by • 0
1
vote
2
replies
870
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 16 months ago by ★ 4.1k • written 16 months ago by • 0
3
votes
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 17 months ago by 68k • written 18 months ago by ▴ 10
0
votes
1
reply
877
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 18 months ago by ▴ 30 • written 6.6 years ago by ▴ 180
0
votes
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
758
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 19 months ago by 68k • written 19 months ago by ▴ 30
5
votes
13
replies
4.1k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
19 months ago fernanda.backsouza ▴ 30
2
votes
2
replies
1.6k
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 19 months ago by 68k • written 19 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
618
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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720
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 20 months ago by ▴ 10
4
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4
replies
5.2k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 20 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
716
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 22 months ago by 68k • written 22 months ago by • 0
4
votes
2
replies
1.3k
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
2.0 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 • updated 2.1 years ago georgii.vdovin • 0
0
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0
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879
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 • updated 2.2 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
288 results • Page 1 of 6
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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.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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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