Showing : clusterProfiler • reset
8
votes
5
replies
4.0k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
5.0 years ago • updated 22 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 2.3 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 15 months ago by 50k • written 16 months ago by ▴ 30
6
votes
11
replies
7.7k
views
Cluster profiler - KEGG analysis
clusterprofiler
3.8 years ago sunnykevin97 • 0
6
votes
2
replies
4.2k
views
help with clusterProfiler enricher function
clusterprofiler
8.0 years ago naholi.alejandri ▴ 50
5
votes
13
replies
4.1k
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
2
replies
333
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
3
replies
3.8k
views
clusterProfiler: Which GO version is used behind ?
clusterProfiler
updated 6.6 years ago by ★ 3.9k • written 6.6 years ago by ▴ 40
4
votes
4
replies
4.1k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 18 months ago by • 0 • written 7.6 years ago by ▴ 660
4
votes
6
replies
3.6k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 19 months ago by ★ 3.9k • written 22 months ago by ▴ 10
4
votes
1
reply
3.2k
views
GSEA using clusterprofileR
clusterprofiler gsea
updated 6.5 years ago by ▴ 240 • written 6.5 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
1
reply
5.9k
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
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 29 days ago by • 0 • written 6.3 years ago by ▴ 20
4
votes
2
replies
4.3k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 13 months ago by ▴ 50 • written 13 months ago by • 0
4
votes
2
replies
6.6k
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
4
replies
6.7k
views
what the test method for enrichGO in clusterProfiler?
clusterProfiler
2.4 years ago • updated 2.3 years ago xiaofeiwang18266 ▴ 50
3
votes
5
replies
1.9k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.1 years ago thomasjenner333 • 0
3
votes
5
replies
3.1k
views
how to color specific node or gene symbol from cnetplot ?
clusterProfiler enrichplot cnetplot GuangchuangYu
updated 19 months ago by ★ 1.2k • written 22 months ago by ▴ 30
3
votes
3
replies
4.6k
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
2
replies
1.0k
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
3.1k
views
gseGO input list
clusterProfiler
2.5 years ago leakerb • 0
3
votes
4
replies
3.9k
views
Sort clusterProfiler result
clusterProfiler sort
updated 6.8 years ago by • 0 • written 8.6 years ago by ▴ 10
3
votes
7
replies
4.5k
views
clusterProfiler - GeneRatio & nb of genes always positively correlated in dotplot
clusterProfiler
7.4 years ago Jane Merlevede ▴ 90
3
votes
2
replies
4.7k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 6.4 years ago by ★ 1.2k • written 6.4 years ago by ▴ 10
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
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 8.4 years ago by ★ 1.6k • written 8.4 years ago by ▴ 830
3
votes
6
replies
2.0k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 4 months ago by 65k • written 18 months ago by ▴ 10
3
votes
11
replies
4.9k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 10 weeks ago by ★ 3.9k • written 3.2 years ago by • 0
3
votes
1
reply
5.8k
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 5.1 years ago by ▴ 10
3
votes
4
replies
1.1k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 5 months ago by ★ 3.9k • written 5 months ago by • 0
2
votes
4
replies
2.1k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 16 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 7.6 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
175
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 25 days ago by ★ 3.9k • written 27 days ago by ▴ 10
2
votes
1
reply
2.0k
views
enrichKEGG
clusterProfiler enrichKEGG
updated 24 months ago by ★ 3.9k • written 24 months ago by • 0
2
votes
2
replies
3.4k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE clusterprofiler annotation gene ontology gene set enrichment
updated 6.4 years ago by ★ 1.2k • written 6.4 years ago by ▴ 10
2
votes
5
replies
3.5k
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
6.4 years ago giuseppe0525 • 0
2
votes
2
replies
3.9k
views
Bgratio column in clusterProfiler enrichGO results
clusterprofiler
updated 8 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
3.2k
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
3.1k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.3 years ago by • 0
2
votes
2
replies
3.2k
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
8
replies
1.6k
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 3.2 years ago by 65k • written 3.2 years ago by ▴ 30
2
votes
2
replies
4.2k
views
How can I visualize Gene Set Enrichment Results from gseGo fun. (clusterProfiler)?
ggplot2 clusterprofiler visualization gseGo
7.0 years ago • updated 3.4 years ago tcalvo ▴ 90
50 results • Page 1 of 1
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Comment: Finding DEGs by using edgeR by Gordon Smyth 50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
Answer: How to make DGEList and design matrix by edgeR package by Gordon Smyth 50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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