Showing : clusterProfiler • reset
0
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1
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164
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Error in cnetplot
enrichplot clusterProfiler
updated 8 days ago by ★ 4.1k • written 14 days ago by • 0
0
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1
reply
227
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
7 weeks ago Jessica • 0
0
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4
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564
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
10 weeks ago Quang NN ▴ 10
2
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2
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623
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 5 months ago by ★ 1.2k • written 5 months ago by • 0
7
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9
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1.5k
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clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 6 months ago by ★ 4.1k • written 6 months ago by • 0
0
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5
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1.0k
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 6 months ago by ▴ 760 • written 6 months ago by • 0
1
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2
replies
2.1k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 7 months ago by • 0
0
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1
reply
852
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
1
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5
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1.6k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 7 months ago by • 0
2
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4
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1.1k
views
# Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.
clusterProfiler makeOrgPackage gseGO
updated 7 months ago by 68k • written 7 months ago by • 0
1
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2
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588
views
Question on number of genes used in GO analysis
GO clusterProfiler
8 months ago Danté • 0
1
vote
1
reply
888
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis clusterProfiler viewPathway gsePathway
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
3
votes
1
reply
1.5k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 9 months ago by ★ 4.1k • written 9 months ago by ▴ 10
1
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2
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899
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
9 months ago sawa • 0
1
vote
9
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2.3k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 9 months ago by 68k • written 9 months ago by ▴ 10
0
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1
reply
618
views
How can I get gseGO to return all GO terms tested?
clusterProfiler clusterp
updated 9 months ago by 68k • written 9 months ago by • 0
8
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6
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7.4k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 10 months ago by ▴ 30 • written 5.9 years ago by ▴ 180
0
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4
replies
980
views
error running enricher from clusterprofiler
clusterProfiler cluster
10 months ago Yael • 0
0
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1
reply
1.1k
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
1
vote
1
reply
471
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 11 months ago by 68k • written 11 months ago by ▴ 30
5
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13
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3.0k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
11 months ago fernanda.backsouza ▴ 30
2
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2
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1.1k
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 11 months ago by 68k • written 11 months ago by • 0
1
vote
2
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1.7k
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
11 months ago Ana • 0
2
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4
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1.6k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 11 months ago by • 0
0
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1
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1.8k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
0
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1
reply
474
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 11 months ago by 68k • written 12 months ago by • 0
0
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0
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511
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
12 months ago andromeda • 0
2
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2
replies
1.1k
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 12 months ago by ▴ 10
4
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4
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4.7k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 12 months ago by • 0 • written 7.3 years ago by ▴ 20
2
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2
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1.3k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
12 months ago Eva ▴ 10
3
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9
replies
6.0k
views
enrichGOgradient color change
clusterProfiler
updated 3 months ago by • 0 • written 16 months ago by • 0
1
vote
1
reply
517
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 13 months ago by 68k • written 13 months ago by • 0
2
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15
replies
1.9k
views
Problems with enrichGO
clusterProfiler enrichGO
updated 13 months ago by 43k • written 13 months ago by • 0
0
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3
replies
1.3k
views
Unable to install clusterProfiler
clusterProfiler
updated 13 months ago by • 0 • written 14 months ago by • 0
0
votes
2
replies
1.0k
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
14 months ago mello-vieira • 0
0
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1
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1.0k
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 14 months ago by 68k • written 14 months ago by • 0
4
votes
2
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984
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
votes
3
replies
2.0k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
3
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6
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3.7k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 16 months ago by 68k • written 2.4 years ago by ▴ 10
0
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9
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1.6k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
16 months ago nromerov • 0
2
votes
9
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3.1k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 17 months ago by ▴ 50 • written 17 months ago by ▴ 30
3
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4
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2.3k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
0
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2
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886
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
17 months ago georgii.vdovin • 0
0
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0
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734
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
17 months ago nromerov • 0
0
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2
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1.7k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 18 months ago by 68k • written 18 months ago by • 0
1
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2
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1.8k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
19 months ago • updated 18 months ago fluentin44 • 0
0
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2
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2.8k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
19 months ago Valéria • 0
3
votes
2
replies
2.3k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 19 months ago by ★ 4.1k • written 19 months ago by ▴ 10
0
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3
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2.6k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 17 months ago by • 0 • written 20 months ago by • 0
0
votes
3
replies
3.2k
views
Not able to install clusterProfiler
clusterProfiler
updated 13 months ago by • 0 • written 20 months ago by • 0
50 results • Page 1 of 1
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Answer: compute_fasta_digest does not match Salmon index hash by Michael Love 43k
Can you provide more details on when this is happening? The salmon index is the definitive hash associated with the quant files, so I'm con…
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species by James W. MacDonald 68k
Oh wait. You want to map from Ensembl to NCBI? That's hard to do with model organisms, let alone non-model. This `OrgDb` doesn't have Ensem…
Answer: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species by James W. MacDonald 68k
You can use the `AnnotationHub` ``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% sna…
Answer: List of Deprecated Packages for Bioc3.20 by shepherl 4.1k
HTqPCR has been fixed and will be re-instated in 3.21
Comment: Question about using LRT test for time course experiments with DESeq2 by Rob • 0
Just to pick up on this thread as its really helpful for understanding the LRT test. The LRT test is given any genes that change within the…
Votes
what the test method for enrichGO in clusterProfiler?
A: single-cells RNA-seq analysis by MAST with unbalanced group size
Comment: plyranges: find exact GRanges match keeping metadata columns
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
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