Showing : ClusterProfiler • reset
3
votes
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
522
views
Error in cnetplot
enrichplot clusterProfiler
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
0
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1
reply
722
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
8 months ago Jessica • 0
0
votes
4
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933
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
870
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
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9
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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
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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
830
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
3.1k
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
817
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
714
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
3.8k
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
2.6k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 9 weeks ago by • 0 • written 18 months ago by • 0
0
votes
1
reply
589
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 18 months ago by 68k • written 19 months ago by • 0
0
votes
0
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668
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
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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 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
7.9k
views
enrichGOgradient color change
clusterProfiler
updated 10 months ago by • 0 • written 23 months ago by • 0
1
vote
1
reply
690
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 20 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
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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
2.0k
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
2.0 years ago georgii.vdovin • 0
0
votes
0
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861
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: 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
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions by Michael Love 43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
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