Showing : ClusterProfiler • reset
0
votes
2
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94
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
18 hours ago • updated 10 hours ago QN ▴ 10
2
votes
2
replies
451
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 11 weeks ago by ★ 1.2k • written 12 weeks ago by • 0
7
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9
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1.3k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
votes
5
replies
778
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 3 months ago by ▴ 760 • written 4 months ago by • 0
1
vote
2
replies
1.3k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 4 months ago by • 0
0
votes
1
reply
594
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
1
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5
replies
1.3k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 5 months ago by • 0
2
votes
4
replies
888
views
# Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.
clusterProfiler makeOrgPackage gseGO
updated 4 months ago by 67k • written 5 months ago by • 0
1
vote
2
replies
442
views
Question on number of genes used in GO analysis
GO clusterProfiler
5 months ago Danté • 0
1
vote
1
reply
601
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis clusterProfiler viewPathway gsePathway
updated 6 months ago by ★ 4.1k • written 6 months ago by • 0
3
votes
1
reply
1.1k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 6 months ago by ★ 4.1k • written 6 months ago by ▴ 10
1
vote
2
replies
741
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
7 months ago sawa • 0
1
vote
9
replies
1.7k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 7 months ago by 67k • written 7 months ago by ▴ 10
0
votes
1
reply
472
views
How can I get gseGO to return all GO terms tested?
clusterProfiler clusterp
updated 7 months ago by 67k • written 7 months ago by • 0
8
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6
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6.4k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 8 months ago by ▴ 30 • written 5.7 years ago by ▴ 160
0
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4
replies
721
views
error running enricher from clusterprofiler
clusterProfiler cluster
8 months ago Yael • 0
0
votes
1
reply
810
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
1
vote
1
reply
408
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 9 months ago by 67k • written 9 months ago by ▴ 30
5
votes
13
replies
2.4k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
9 months ago fernanda.backsouza ▴ 30
2
votes
2
replies
851
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 9 months ago by 67k • written 9 months ago by • 0
1
vote
2
replies
1.3k
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
9 months ago Ana • 0
2
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3
replies
1.0k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
updated 9 weeks ago by • 0 • written 9 months ago by • 0
0
votes
1
reply
1.4k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
0
votes
1
reply
415
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 9 months ago by 67k • written 9 months ago by • 0
0
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0
replies
448
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
9 months ago andromeda • 0
2
votes
2
replies
846
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 10 months ago by ▴ 10
4
votes
4
replies
4.5k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 10 months ago by • 0 • written 7.1 years ago by ▴ 20
2
votes
2
replies
1.0k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
10 months ago Eva ▴ 10
2
votes
9
replies
4.9k
views
enrichGOgradient color change
clusterProfiler
updated 19 days ago by • 0 • written 14 months ago by • 0
1
vote
1
reply
449
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 11 months ago by 67k • written 11 months ago by • 0
2
votes
15
replies
1.5k
views
Problems with enrichGO
clusterProfiler enrichGO
updated 11 months ago by 43k • written 11 months ago by • 0
0
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3
replies
1.1k
views
Unable to install clusterProfiler
clusterProfiler
updated 11 months ago by • 0 • written 11 months ago by • 0
0
votes
2
replies
904
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
11 months ago mello-vieira • 0
0
votes
1
reply
833
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 12 months ago by 67k • written 12 months ago by • 0
4
votes
2
replies
877
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
0
votes
3
replies
1.8k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
3
votes
6
replies
3.3k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 13 months ago by 67k • written 2.2 years ago by ▴ 10
0
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9
replies
1.4k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
14 months ago • updated 13 months ago nromerov • 0
2
votes
9
replies
3.0k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 14 months ago by ▴ 50 • written 15 months ago by ▴ 30
3
votes
4
replies
2.0k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
0
votes
2
replies
814
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
15 months ago georgii.vdovin • 0
0
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0
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643
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
15 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 16 months ago by 67k • written 16 months ago by • 0
1
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2
replies
1.5k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
16 months ago fluentin44 • 0
0
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2
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2.3k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
17 months ago • updated 16 months ago Valéria • 0
3
votes
2
replies
2.0k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 17 months ago by ★ 4.1k • written 17 months ago by ▴ 10
0
votes
3
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2.3k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 15 months ago by • 0 • written 17 months ago by • 0
0
votes
3
replies
2.7k
views
Not able to install clusterProfiler
clusterProfiler
updated 11 months ago by • 0 • written 18 months ago by • 0
0
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0
replies
552
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
18 months ago georgii.vdovin • 0
2
votes
5
replies
3.8k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 4.0 years ago by • 0
50 results • Page 1 of 1
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Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 740
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Votes
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
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