Showing : ClusterProfiler • reset
2
votes
2
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416
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clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 7 weeks ago by ★ 1.2k • written 8 weeks ago by • 0
7
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9
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1.2k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
0
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5
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680
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 12 weeks ago by ▴ 760 • written 3 months ago by • 0
1
vote
2
replies
1.1k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 3 months ago by • 0
0
votes
1
reply
513
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
1
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5
replies
1.1k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 4 months ago by • 0
2
votes
4
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819
views
# Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.
clusterProfiler makeOrgPackage gseGO
updated 3 months ago by 67k • written 4 months ago by • 0
1
vote
2
replies
397
views
Question on number of genes used in GO analysis
GO clusterProfiler
4 months ago Danté • 0
1
vote
1
reply
520
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis clusterProfiler viewPathway gsePathway
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
3
votes
1
reply
999
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 5 months ago by ★ 4.1k • written 5 months ago by ▴ 10
1
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2
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693
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
6 months ago sawa • 0
1
vote
9
replies
1.5k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 6 months ago by 67k • written 6 months ago by ▴ 10
0
votes
1
reply
425
views
How can I get gseGO to return all GO terms tested?
clusterProfiler clusterp
updated 6 months ago by 67k • written 6 months ago by • 0
8
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6
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6.2k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 6 months ago by ▴ 30 • written 5.6 years ago by ▴ 160
0
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4
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648
views
error running enricher from clusterprofiler
clusterProfiler cluster
7 months ago Yael • 0
0
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1
reply
746
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
1
vote
1
reply
377
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 7 months ago by 67k • written 7 months ago by ▴ 30
5
votes
13
replies
2.1k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
8 months ago • updated 7 months ago fernanda.backsouza ▴ 30
2
votes
2
replies
788
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 8 months ago by 67k • written 8 months ago by • 0
1
vote
2
replies
1.2k
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
8 months ago Ana • 0
2
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3
replies
893
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
updated 5 weeks ago by • 0 • written 8 months ago by • 0
0
votes
1
reply
1.2k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
1
reply
389
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 8 months ago by 67k • written 8 months ago by • 0
0
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0
replies
425
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
8 months ago andromeda • 0
2
votes
2
replies
773
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 9 months ago by ▴ 10
4
votes
4
replies
4.4k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 9 months ago by • 0 • written 7.0 years ago by ▴ 20
2
votes
2
replies
923
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
9 months ago Eva ▴ 10
1
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8
replies
4.4k
views
enrichGOgradient color change
clusterProfiler
updated 6 months ago by • 0 • written 13 months ago by • 0
1
vote
1
reply
425
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 10 months ago by 67k • written 10 months ago by • 0
2
votes
15
replies
1.4k
views
Problems with enrichGO
clusterProfiler enrichGO
updated 10 months ago by 43k • written 10 months ago by • 0
0
votes
3
replies
1.0k
views
Unable to install clusterProfiler
clusterProfiler
updated 10 months ago by • 0 • written 10 months ago by • 0
0
votes
2
replies
842
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
10 months ago mello-vieira • 0
0
votes
1
reply
765
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 10 months ago by 67k • written 10 months ago by • 0
4
votes
2
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828
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
0
votes
3
replies
1.7k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
3
votes
6
replies
3.2k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 12 months ago by 67k • written 2.2 years ago by ▴ 10
0
votes
9
replies
1.3k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
12 months ago nromerov • 0
2
votes
9
replies
2.9k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 13 months ago by ▴ 50 • written 13 months ago by ▴ 30
3
votes
4
replies
1.9k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
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2
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784
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
14 months ago georgii.vdovin • 0
0
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0
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617
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
14 months ago nromerov • 0
0
votes
2
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1.4k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 14 months ago by 67k • written 14 months ago by • 0
1
vote
2
replies
1.5k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
15 months ago fluentin44 • 0
0
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2
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2.2k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
16 months ago • updated 15 months ago Valéria • 0
3
votes
2
replies
1.9k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 16 months ago by ★ 4.1k • written 16 months ago by ▴ 10
0
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3
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2.2k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 14 months ago by • 0 • written 16 months ago by • 0
0
votes
3
replies
2.5k
views
Not able to install clusterProfiler
clusterProfiler
updated 10 months ago by • 0 • written 17 months ago by • 0
0
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0
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531
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
17 months ago georgii.vdovin • 0
2
votes
5
replies
3.8k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.9 years ago by • 0
0
votes
1
reply
1.5k
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO GeneSet clusterProfiler GeneSetEnrichment
updated 17 months ago by 67k • written 17 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: nightmare to make custom txdb for genomes from ToxoDB by Hervé Pagès 16k
`keepStandardChromosomes()` is not smart enough to know what to keep for this assembly. Note that what `keepStandardChromosomes()` means by…
Comment: nightmare to make custom txdb for genomes from ToxoDB by James W. MacDonald 67k
Thanks Hervé! Very helpful. However, I believe that `keepStandardChromosomes` gets called by `gDNAx`, and it appears not to work correctly.…
Answer: nightmare to make custom txdb for genomes from ToxoDB by Hervé Pagès 16k
Is this for genome assembly TGA4? https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000006565.2/ If that's the case then: ``` library(t…
Answer: nightmare to make custom txdb for genomes from ToxoDB by James W. MacDonald 67k
Your post title is misleading. You have no problem whatsoever generating the `TxDb`, the problem is using it with `gDNAx`, which attempts t…
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
Just fit a model `~condition + experiment` where `condition` has three levels A, B and C. Ideally, use limma and include duplicate correlat…
Votes
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
Comment: Feature Counts - potential bug with outfile.jcounts
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Scholar to James W. MacDonald 67k
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