Showing : clusterprofiler • reset
8
votes
6
replies
4.3k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 6 days ago by ▴ 30 • written 5.1 years ago by ▴ 160
0
votes
4
replies
195
views
error running enricher from clusterprofiler
clusterProfiler cluster
14 days ago Yael • 0
0
votes
1
reply
216
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 16 days ago by ★ 4.0k • written 17 days ago by • 0
1
vote
1
reply
148
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 5 weeks ago by 66k • written 5 weeks ago by ▴ 10
2
votes
13
replies
576
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
5 weeks ago fernanda.backsouza ▴ 10
2
votes
2
replies
253
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 5 weeks ago by 66k • written 5 weeks ago by • 0
1
vote
2
replies
204
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
6 weeks ago Ana • 0
2
votes
2
replies
238
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
6 weeks ago julia_mcdonough • 0
0
votes
1
reply
228
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 6 weeks ago by ★ 4.0k • written 7 weeks ago by • 0
0
votes
1
reply
201
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 7 weeks ago by 66k • written 7 weeks ago by • 0
0
votes
0
replies
169
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
7 weeks ago andromeda • 0
2
votes
1
reply
255
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 9 weeks ago by ★ 4.0k • written 9 weeks ago by ▴ 10
4
votes
4
replies
3.8k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 10 weeks ago by • 0 • written 6.5 years ago by ▴ 20
2
votes
2
replies
322
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
10 weeks ago Eva ▴ 10
1
vote
8
replies
1.8k
views
enrichGOgradient color change
clusterProfiler
updated 6 days ago by • 0 • written 6 months ago by • 0
1
vote
1
reply
225
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 3 months ago by 66k • written 3 months ago by • 0
2
votes
15
replies
759
views
Problems with enrichGO
clusterProfiler enrichGO
updated 3 months ago by 42k • written 3 months ago by • 0
0
votes
3
replies
488
views
Unable to install clusterProfiler
clusterProfiler
updated 3 months ago by • 0 • written 3 months ago by • 0
0
votes
2
replies
384
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
3 months ago mello-vieira • 0
0
votes
1
reply
351
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 4 months ago by 66k • written 4 months ago by • 0
4
votes
2
replies
426
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
0
votes
3
replies
933
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
3
votes
6
replies
2.2k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 6 months ago by 66k • written 19 months ago by ▴ 10
0
votes
9
replies
739
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
6 months ago nromerov • 0
2
votes
9
replies
1.3k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 7 months ago by ▴ 50 • written 7 months ago by ▴ 30
3
votes
4
replies
1.3k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
0
votes
2
replies
520
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
7 months ago georgii.vdovin • 0
0
votes
0
replies
398
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
7 months ago nromerov • 0
0
votes
2
replies
727
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 8 months ago by 66k • written 8 months ago by • 0
1
vote
2
replies
935
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
8 months ago fluentin44 • 0
0
votes
2
replies
1.3k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
9 months ago Valéria • 0
3
votes
2
replies
1.2k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
0
votes
3
replies
1.4k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 7 months ago by • 0 • written 9 months ago by • 0
0
votes
3
replies
1.6k
views
Not able to install clusterProfiler
clusterProfiler
updated 3 months ago by • 0 • written 10 months ago by • 0
0
votes
0
replies
370
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
10 months ago georgii.vdovin • 0
2
votes
5
replies
3.3k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.4 years ago by • 0
0
votes
1
reply
913
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO GeneSet clusterProfiler GeneSetEnrichment
updated 10 months ago by 66k • written 10 months ago by • 0
0
votes
5
replies
1.1k
views
plot enrichment results
enrichplot clusterProfiler
updated 10 months ago by ▴ 730 • written 11 months ago by • 0
0
votes
2
replies
716
views
Question regarding FAQ
clusterProfiler
11 months ago kl-fr • 0
0
votes
0
replies
894
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
12 months ago pg45863 ▴ 10
2
votes
4
replies
1.6k
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot clusterProfiler
12 months ago Tyroone • 0
0
votes
1
reply
1.2k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 13 months ago by 3.9k • written 13 months ago by • 0
0
votes
5
replies
1.4k
views
enrichKEGG function error
cluster clusterProfiler KEGG
13 months ago • updated 12 months ago ruba-mahmoud • 0
1
vote
3
replies
1.2k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 13 months ago by ★ 4.0k • written 14 months ago by ▴ 10
0
votes
1
reply
621
views
what does "exp1" mean in the gage() function?
gage clusterProfiler DESeq2
updated 14 months ago by 66k • written 14 months ago by ▴ 10
1
vote
3
replies
4.1k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 14 months ago by ★ 4.0k • written 15 months ago by ▴ 10
0
votes
1
reply
1.2k
views
Am I able to add gene names/symbols to an enrichGO() output?
clusterProfiler enrichplot
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
1
vote
3
replies
917
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 5 weeks ago by ★ 1.2k • written 15 months ago by ▴ 10
4
votes
2
replies
4.6k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 15 months ago by ▴ 50 • written 15 months ago by • 0
1
vote
7
replies
2.0k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 15 months ago by ▴ 780 • written 15 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: How to run allelic imbalance in apeglm by parayod376 • 0
Which I care about. [Papa's games][1] thank you for sharing the information. [1]: https://papasgamesfree.github.io
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
FYI, I emailed Benilton and he says he's working on a fix, so stay tuned!
Answer: Error in render R qmd document (could not find function "process") by James W. MacDonald 66k
If you have functions in another R document, you have to `source` that document to load the functions into your workspace. Just like you wo…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
Thank you! I ended up running it with a gtf on command line, partially because I couldn't figure out how to list multiple files in R for in…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
For some reason, that's still not working for me on command line. I ended up figuring out another way around, though, by converting the g…
Votes
Reduce the number of nodes appear in the cnetplot of clusterprofiler
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
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