Showing : clusterprofiler • reset
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OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 1 day ago by 65k • written 1 day ago by • 0
1
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2
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89
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geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
4 days ago Ana • 0
2
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2
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152
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
8 days ago • updated 7 days ago julia_mcdonough • 0
0
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1
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117
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compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 6 days ago by ★ 3.9k • written 9 days ago by • 0
0
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1
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150
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How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 12 days ago by 65k • written 12 days ago by • 0
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0
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125
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Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
15 days ago • updated 14 days ago andromeda • 0
2
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1
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180
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Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 27 days ago by ★ 3.9k • written 28 days ago by ▴ 10
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4
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3.7k
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Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 4 weeks ago by • 0 • written 6.4 years ago by ▴ 20
2
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2
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235
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padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
4 weeks ago Eva ▴ 10
1
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7
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1.4k
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enrichGOgradient color change
clusterProfiler
updated 4 weeks ago by ★ 3.9k • written 5 months ago by • 0
1
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1
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175
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Clsuter Profiler "counts"
enrich clusterProfiler
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
2
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15
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636
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Problems with enrichGO
clusterProfiler enrichGO
updated 9 weeks ago by 41k • written 10 weeks ago by • 0
0
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3
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378
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Unable to install clusterProfiler
clusterProfiler
updated 9 weeks ago by • 0 • written 10 weeks ago by • 0
0
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2
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290
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Problem with buildGOmap from clusterProfiler
clusterProfiler
10 weeks ago mello-vieira • 0
0
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1
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251
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ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
4
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2
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335
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Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 3 months ago by ★ 3.9k • written 3 months ago by • 0
0
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3
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760
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How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 4 months ago by ★ 3.9k • written 4 months ago by • 0
3
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6
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2.0k
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Result from GSEA for non-model organism not as expected
clusterProfiler
updated 4 months ago by 65k • written 18 months ago by ▴ 10
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9
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607
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It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
4 months ago nromerov • 0
2
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9
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1.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 5 months ago by ▴ 50 • written 5 months ago by ▴ 30
3
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4
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1.1k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 5 months ago by ★ 3.9k • written 5 months ago by • 0
0
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2
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448
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Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
6 months ago georgii.vdovin • 0
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0
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345
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clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
6 months ago nromerov • 0
0
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2
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605
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For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 6 months ago by 65k • written 6 months ago by • 0
1
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2
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816
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
7 months ago fluentin44 • 0
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2
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1.1k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
7 months ago Valéria • 0
3
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2
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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
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3
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1.2k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 5 months ago by • 0 • written 8 months ago by • 0
0
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3
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1.4k
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Not able to install clusterProfiler
clusterProfiler
updated 9 weeks ago by • 0 • written 9 months ago by • 0
0
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0
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338
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Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
9 months ago georgii.vdovin • 0
2
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5
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3.1k
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How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.3 years ago by • 0
0
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1
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755
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How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO GeneSet clusterProfiler GeneSetEnrichment
updated 9 months ago by 65k • written 9 months ago by • 0
0
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5
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988
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plot enrichment results
enrichplot clusterProfiler
updated 9 months ago by ▴ 730 • written 9 months ago by • 0
0
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2
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658
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Question regarding FAQ
clusterProfiler
10 months ago kl-fr • 0
0
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0
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808
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fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
10 months ago pg45863 ▴ 10
2
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4
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1.4k
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot clusterProfiler
11 months ago Tyroone • 0
0
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1
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1.0k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 12 months ago by 3.8k • written 12 months ago by • 0
0
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5
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1.3k
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enrichKEGG function error
cluster clusterProfiler KEGG
12 months ago • updated 11 months ago ruba-mahmoud • 0
1
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3
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1.1k
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how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 12 months ago by ★ 3.9k • written 12 months ago by ▴ 10
0
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1
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588
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what does "exp1" mean in the gage() function?
gage clusterProfiler DESeq2
updated 12 months ago by 65k • written 12 months ago by ▴ 10
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3
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3.7k
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Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 13 months ago by ★ 3.9k • written 14 months ago by • 0
0
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1
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1.2k
views
Am I able to add gene names/symbols to an enrichGO() output?
clusterProfiler enrichplot
updated 13 months ago by ★ 3.9k • written 13 months ago by • 0
1
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2
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755
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 1 day ago by • 0 • written 13 months ago by ▴ 10
4
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2
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4.3k
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gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 13 months ago by ▴ 50 • written 13 months ago by • 0
1
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7
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1.8k
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Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 13 months ago by ▴ 770 • written 13 months ago by ▴ 10
2
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6
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1.9k
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clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 3 months ago by ★ 3.9k • written 13 months ago by ▴ 10
0
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1
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645
views
Libraries loading error
DESeq2 clusterProfiler enrichplot
updated 15 months ago by 41k • written 15 months ago by • 0
0
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2
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2.0k
views
clusterProfiler - custom annotations
clusterProfiler
updated 3 months ago by ★ 3.9k • written 16 months ago by • 0
1
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1
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1.1k
views
How to include background "universe" in compareCluster function of clusterprofiler package
clusterProfiler
updated 16 months ago by ▴ 770 • written 16 months ago by • 0
1
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7
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1.4k
views
Adding geneID to list of gene locus IDs
cluster OrgDb clusterProfiler
written 17 months ago by • 0
50 results • Page 1 of 1
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Answer: Why p value inconsistent when using different number of pathway score? by ATpoint ★ 4.0k
Same answer as here: https://support.bioconductor.org/p/9157606/ Adding or removing data (samples, genes, pathways, observations...) chang…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
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