Showing : ClusterProfiler • reset
8
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5
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4.1k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
5.0 years ago • updated 23 months ago charles.foster ▴ 160
8
votes
9
replies
8.9k
views
Error: package or namespace load failed for ‘clusterProfiler’: object ‘get_fun_from_pkg’ is not exported by 'namespace:rvcheck'
get_fun_from_pkg clusterProfiler rvcheck
updated 2.4 years ago by • 0 • written 2.6 years ago by • 0
7
votes
6
replies
2.1k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 16 months ago by 50k • written 17 months ago by ▴ 30
6
votes
2
replies
4.3k
views
help with clusterProfiler enricher function
clusterprofiler
8.0 years ago naholi.alejandri ▴ 50
6
votes
11
replies
7.8k
views
Cluster profiler - KEGG analysis
clusterprofiler
3.8 years ago sunnykevin97 • 0
5
votes
13
replies
4.2k
views
Getting error
enrichplot clusterProfiler org.Hs.eg.db
updated 2.1 years ago by ▴ 40 • written 2.1 years ago by • 0
4
votes
1
reply
3.3k
views
GSEA using clusterprofileR
clusterprofiler gsea
updated 6.5 years ago by ▴ 260 • written 6.5 years ago by ▴ 30
4
votes
2
replies
4.4k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 14 months ago by ▴ 50 • written 14 months ago by • 0
4
votes
3
replies
3.8k
views
clusterProfiler: Which GO version is used behind ?
clusterProfiler
updated 6.7 years ago by ★ 3.9k • written 6.7 years ago by ▴ 50
4
votes
2
replies
363
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 3 months ago by ★ 3.9k • written 3 months ago by • 0
4
votes
1
reply
6.0k
views
Warning message as converting gene Symbol to ENTREZID
go clusterprofiler
updated 3.8 years ago by 65k • written 3.8 years ago by ▴ 30
4
votes
10
replies
6.2k
views
Help with enrichKEGG function in clusterProfiler
clusterprofiler
updated 21 months ago by ▴ 40 • written 8.2 years ago by ▴ 10
4
votes
4
replies
4.2k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 18 months ago by • 0 • written 7.7 years ago by ▴ 660
4
votes
2
replies
6.7k
views
How to export enrichGO results for future visualization with barplot, dotplot, emapplot...
clusterprofiler enrichGO barplot dotplot
5.7 years ago MAP • 0
4
votes
6
replies
3.7k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 20 months ago by ★ 3.9k • written 22 months ago by ▴ 10
4
votes
4
replies
3.7k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 6 weeks ago by • 0 • written 6.4 years ago by ▴ 20
4
votes
4
replies
6.9k
views
what the test method for enrichGO in clusterProfiler?
clusterProfiler
2.4 years ago xiaofeiwang18266 ▴ 50
3
votes
5
replies
2.0k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.1 years ago thomasjenner333 • 0
3
votes
5
replies
3.2k
views
how to color specific node or gene symbol from cnetplot ?
clusterProfiler enrichplot cnetplot GuangchuangYu
updated 20 months ago by ★ 1.2k • written 23 months ago by ▴ 30
3
votes
3
replies
4.7k
views
Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 10 months ago by ★ 3.9k • written 4.0 years ago by • 0
3
votes
4
replies
3.9k
views
Sort clusterProfiler result
clusterProfiler sort
updated 6.8 years ago by • 0 • written 8.7 years ago by ▴ 10
3
votes
2
replies
1.1k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 8 months ago by ★ 3.9k • written 8 months ago by ▴ 10
3
votes
2
replies
4.8k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by ▴ 10
3
votes
7
replies
4.5k
views
clusterProfiler - GeneRatio & nb of genes always positively correlated in dotplot
clusterProfiler
7.5 years ago Jane Merlevede ▴ 90
3
votes
4
replies
1.2k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 6 months ago by ★ 3.9k • written 6 months ago by • 0
3
votes
2
replies
3.2k
views
gseGO input list
clusterProfiler
2.5 years ago leakerb • 0
3
votes
5
replies
2.3k
views
Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
pathview clusterProfiler KEGGpath visualization Graphviz
updated 8.5 years ago by ★ 1.6k • written 8.5 years ago by ▴ 830
3
votes
3
replies
3.3k
views
problem reinstalling Bioconductor package 'clusterProfiler' after updating R to 3.4.0
clusterprofiler package installation r update
updated 6.9 years ago by ▴ 10 • written 7.0 years ago by ▴ 10
3
votes
11
replies
5.0k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 12 weeks ago by ★ 3.9k • written 3.2 years ago by • 0
3
votes
1
reply
5.9k
views
clusterProfiler - Non model organism
clusterprofiler
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by ▴ 10
3
votes
4
replies
3.3k
views
error in keytype performing "enrichGO" from clusterprofiler
clusterprofiler
updated 3.1 years ago by ▴ 20 • written 5.2 years ago by ▴ 10
3
votes
6
replies
2.1k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 5 months ago by 65k • written 18 months ago by ▴ 10
2
votes
4
replies
2.1k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 17 months ago by • 0
2
votes
4
replies
3.0k
views
#clusterProfiler# KEGG enrichment with non-reference species
clusterprofiler kaas enrichKEGG
updated 6.8 years ago by • 0 • written 7.7 years ago by • 0
2
votes
2
replies
4.0k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 6.1 years ago by ★ 1.2k • written 6.1 years ago by • 0
2
votes
1
reply
211
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 5 weeks ago by ★ 3.9k • written 6 weeks ago by ▴ 10
2
votes
1
reply
2.1k
views
enrichKEGG
clusterProfiler enrichKEGG
updated 2.0 years ago by ★ 3.9k • written 2.0 years ago by • 0
2
votes
2
replies
3.5k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE clusterprofiler annotation gene ontology gene set enrichment
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by ▴ 10
2
votes
5
replies
3.6k
views
GO enrichment comparison with other programs
clusterprofiler enrichment analysis
updated 7.3 years ago by ★ 1.2k • written 7.3 years ago by ▴ 30
2
votes
3
replies
1.8k
views
custom annotation for GO enrichment
annotationforge GSEA clusterprofiler GO annotation
6.7 years ago cabezasdelafuented ▴ 10
2
votes
6
replies
12k
views
GSEA using clusterProfiler
GSEA clusterProfiler
6.5 years ago giuseppe0525 • 0
2
votes
2
replies
183
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 15 days ago by 65k • written 15 days ago by • 0
2
votes
2
replies
3.3k
views
Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
clusterprofiler
updated 2.4 years ago by • 0 • written 7.4 years ago by ▴ 40
2
votes
2
replies
4.0k
views
Bgratio column in clusterProfiler enrichGO results
clusterprofiler
updated 9 months ago by • 0 • written 7.8 years ago by ▴ 10
2
votes
4
replies
2.5k
views
Problem with BuildGOmap() in clusterProfiler
clusterprofiler
7.4 years ago Marcus • 0
2
votes
4
replies
3.3k
views
I want to make a geneList for clusterProfiler analysis but I get "error in do.call( cbind lapply(x is.na )) variable names are limited to 10000 bytes"
clusterProfiler
3.4 years ago Emilia ▴ 30
2
votes
5
replies
3.2k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.3 years ago by • 0
2
votes
8
replies
1.7k
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error enrichGO annotationHub clusterProfiler Job
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
2
votes
10
replies
12k
views
keytype not supported in clusterprofiler when it is ensembl IDs?
clusterProfiler enrichGO
updated 4.0 years ago by 65k • written 4.0 years ago by ▴ 30
2
votes
3
replies
1.7k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 3.3 years ago by 65k • written 3.3 years ago by ▴ 30
50 results • Page 1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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