Showing : clusterProfiler • reset
3
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4
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5.1k
views
Analysis of clusters of a heatmap with enrichGO of clusterProfiler: choice fo the categories to visualize
clusterProfiler enrichGO ComplexHeatmap
updated 4 months ago by 68k • written 4 months ago by ▴ 10
1
vote
3
replies
1.2k
views
CluserProfiler message "No gene can be mapped"
clusterProfiler
updated 6 months ago by 68k • written 6 months ago by • 0
0
votes
3
replies
1.2k
views
Gene Ontology (GO) Analysis
GOstats hyperGTest GO enrichGO clusterProfiler
6 months ago • updated 5 months ago GA ▴ 10
0
votes
1
reply
538
views
Error in cnetplot
enrichplot clusterProfiler
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
0
votes
1
reply
727
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
8 months ago Jessica • 0
0
votes
4
replies
937
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
9 months ago Quang NN ▴ 10
2
votes
2
replies
879
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 12 months ago by ★ 1.2k • written 12 months ago by • 0
7
votes
9
replies
1.9k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
votes
5
replies
1.4k
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 13 months ago by ▴ 760 • written 13 months ago by • 0
1
vote
2
replies
3.0k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 14 months ago by • 0
0
votes
1
reply
1.3k
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
1
vote
5
replies
2.2k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 14 months ago by • 0
2
votes
4
replies
1.5k
views
# Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.
clusterProfiler makeOrgPackage gseGO
updated 14 months ago by 68k • written 14 months ago by • 0
1
vote
2
replies
835
views
Question on number of genes used in GO analysis
GO clusterProfiler
15 months ago Danté • 0
1
vote
1
reply
1.3k
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis clusterProfiler viewPathway gsePathway
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
3
votes
1
reply
2.0k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 16 months ago by ★ 4.1k • written 16 months ago by ▴ 10
1
vote
2
replies
1.2k
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
16 months ago sawa • 0
1
vote
9
replies
3.2k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 16 months ago by 68k • written 16 months ago by ▴ 10
0
votes
1
reply
823
views
How can I get gseGO to return all GO terms tested?
clusterProfiler clusterp
updated 16 months ago by 68k • written 16 months ago by • 0
8
votes
6
replies
8.7k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 17 months ago by ▴ 30 • written 6.5 years ago by ▴ 180
0
votes
4
replies
1.4k
views
error running enricher from clusterprofiler
clusterProfiler cluster
17 months ago Yael • 0
0
votes
1
reply
1.4k
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
1
vote
1
reply
718
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 18 months ago by 68k • written 18 months ago by ▴ 30
5
votes
13
replies
3.9k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
18 months ago fernanda.backsouza ▴ 30
2
votes
2
replies
1.5k
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 18 months ago by 68k • written 18 months ago by • 0
1
vote
2
replies
2.5k
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
18 months ago Ana • 0
2
votes
4
replies
2.2k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 18 months ago by • 0
0
votes
2
replies
2.7k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 10 weeks ago by • 0 • written 18 months ago by • 0
0
votes
1
reply
591
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
0
replies
675
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
19 months ago andromeda • 0
2
votes
2
replies
1.4k
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 19 months ago by ▴ 10
4
votes
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 19 months ago by • 0 • written 7.9 years ago by ▴ 20
2
votes
2
replies
1.7k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
19 months ago Eva ▴ 10
3
votes
9
replies
8.0k
views
enrichGOgradient color change
clusterProfiler
updated 10 months ago by • 0 • written 23 months ago by • 0
1
vote
1
reply
692
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 20 months ago by 68k • written 20 months ago by • 0
2
votes
15
replies
2.5k
views
Problems with enrichGO
clusterProfiler enrichGO
updated 20 months ago by 43k • written 21 months ago by • 0
0
votes
3
replies
1.6k
views
Unable to install clusterProfiler
clusterProfiler
updated 20 months ago by • 0 • written 21 months ago by • 0
0
votes
2
replies
1.3k
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
21 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 21 months ago by 68k • written 21 months ago by • 0
4
votes
2
replies
1.3k
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 21 months ago by ★ 4.1k • written 21 months ago by • 0
0
votes
3
replies
2.5k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 23 months ago by ★ 4.1k • written 23 months ago by • 0
3
votes
6
replies
4.3k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 23 months ago by 68k • written 3.0 years ago by ▴ 10
0
votes
9
replies
2.1k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
23 months ago nromerov • 0
2
votes
9
replies
3.5k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 2.0 years ago by ▴ 50 • written 2.0 years ago by ▴ 30
3
votes
4
replies
2.8k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 2.0 years ago by ★ 4.1k • written 2.0 years ago by • 0
0
votes
2
replies
1.1k
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
2.1 years ago • updated 2.0 years ago georgii.vdovin • 0
0
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0
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863
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
2.1 years ago nromerov • 0
0
votes
2
replies
2.2k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
vote
2
replies
2.2k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
2.1 years ago fluentin44 • 0
0
votes
2
replies
3.4k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
2.2 years ago Valéria • 0
288 results • Page 1 of 6
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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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