Showing : clusterProfiler • reset
3
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4
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5.3k
views
Analysis of clusters of a heatmap with enrichGO of clusterProfiler: choice fo the categories to visualize
clusterProfiler enrichGO ComplexHeatmap
updated 6 months ago by 68k • written 6 months ago by ▴ 10
1
vote
3
replies
1.3k
views
CluserProfiler message "No gene can be mapped"
clusterProfiler
updated 8 months ago by 68k • written 8 months ago by • 0
0
votes
3
replies
1.4k
views
Gene Ontology (GO) Analysis
GOstats hyperGTest GO enrichGO clusterProfiler
8 months ago GA ▴ 10
0
votes
1
reply
709
views
Error in cnetplot
enrichplot clusterProfiler
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
0
votes
1
reply
816
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
11 months ago Jessica • 0
0
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4
replies
1.1k
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
11 months ago Quang NN ▴ 10
2
votes
2
replies
998
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 14 months ago by ★ 1.2k • written 14 months ago by • 0
7
votes
9
replies
2.1k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
0
votes
5
replies
1.7k
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 15 months ago by ▴ 760 • written 16 months ago by • 0
1
vote
2
replies
3.5k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 16 months ago by • 0
0
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1
reply
1.6k
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
1
vote
5
replies
2.4k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 17 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 16 months ago by 68k • written 17 months ago by • 0
1
vote
2
replies
912
views
Question on number of genes used in GO analysis
GO clusterProfiler
17 months ago Danté • 0
1
vote
1
reply
1.7k
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis clusterProfiler viewPathway gsePathway
updated 18 months ago by ★ 4.1k • written 18 months ago by • 0
3
votes
1
reply
2.3k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 18 months ago by ★ 4.1k • written 18 months ago by ▴ 10
1
vote
2
replies
1.3k
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
19 months ago sawa • 0
1
vote
9
replies
3.7k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 19 months ago by 68k • written 19 months ago by ▴ 10
0
votes
1
reply
947
views
How can I get gseGO to return all GO terms tested?
clusterProfiler clusterp
updated 19 months ago by 68k • written 19 months ago by • 0
8
votes
6
replies
9.6k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 19 months ago by ▴ 30 • written 6.7 years ago by ▴ 180
0
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4
replies
1.6k
views
error running enricher from clusterprofiler
clusterProfiler cluster
20 months ago Yael • 0
0
votes
1
reply
1.7k
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 20 months ago by ★ 4.1k • written 20 months ago by • 0
1
vote
1
reply
792
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
4.3k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
21 months ago • updated 20 months ago fernanda.backsouza ▴ 30
2
votes
2
replies
1.8k
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 21 months ago by 68k • written 21 months ago by • 0
1
vote
2
replies
2.7k
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
21 months ago Ana • 0
2
votes
4
replies
2.5k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 21 months ago by • 0
0
votes
2
replies
3.0k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 4 months ago by • 0 • written 21 months ago by • 0
0
votes
1
reply
651
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
0
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762
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
21 months ago andromeda • 0
2
votes
2
replies
1.5k
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 22 months ago by ▴ 10
4
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4
replies
5.4k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 22 months ago by • 0 • written 8.1 years ago by ▴ 20
2
votes
2
replies
1.9k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
22 months ago Eva ▴ 10
3
votes
9
replies
8.6k
views
enrichGOgradient color change
clusterProfiler
updated 12 months ago by • 0 • written 2.2 years ago by • 0
1
vote
1
reply
752
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 23 months ago by 68k • written 23 months ago by • 0
2
votes
15
replies
2.8k
views
Problems with enrichGO
clusterProfiler enrichGO
updated 23 months ago by 43k • written 23 months ago by • 0
0
votes
3
replies
1.7k
views
Unable to install clusterProfiler
clusterProfiler
updated 23 months ago by • 0 • written 23 months ago by • 0
0
votes
2
replies
1.4k
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
23 months ago mello-vieira • 0
0
votes
1
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1.5k
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 23 months ago by 68k • written 24 months ago by • 0
4
votes
2
replies
1.4k
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 24 months ago by ★ 4.1k • written 24 months ago by • 0
0
votes
3
replies
2.7k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 2.1 years ago by ★ 4.1k • written 2.1 years ago by • 0
3
votes
6
replies
4.5k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 2.1 years ago by 68k • written 3.2 years ago by ▴ 10
0
votes
9
replies
2.4k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
2.1 years ago nromerov • 0
2
votes
9
replies
3.8k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 2.2 years ago by ▴ 50 • written 2.2 years ago by ▴ 30
3
votes
4
replies
3.0k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 2.2 years ago by ★ 4.1k • written 2.2 years ago by • 0
0
votes
2
replies
1.2k
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
2.3 years ago • updated 2.2 years ago georgii.vdovin • 0
0
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0
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921
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
2.3 years ago nromerov • 0
0
votes
2
replies
2.4k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
1
vote
2
replies
2.3k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
2.3 years ago fluentin44 • 0
0
votes
2
replies
3.6k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
2.4 years ago Valéria • 0
288 results • Page 1 of 6
Recent ...
Replies
Answer: Confounded design, batch effect correction (edgeR) by nig.httopss • 0
To perform gene matching accurately, you should use the formula ~0 + Group + Batch in the design matrix to better manage sample groups. Sin…
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 10
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Comment: Incosistencies in buildSNNGraph() function by ATpoint ★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Answer: Incosistencies in buildSNNGraph() function by Aaron Lun ★ 29k
The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Votes
Answer: Clarification on counting in Rsubread (featureCounts)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
A: Conversion from counts to FPKM
Answer: Incosistencies in buildSNNGraph() function
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