Showing : clusterProfiler • reset
3
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4
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5.1k
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Analysis of clusters of a heatmap with enrichGO of clusterProfiler: choice fo the categories to visualize
clusterProfiler enrichGO ComplexHeatmap
updated 11 weeks ago by 68k • written 12 weeks ago by ▴ 10
1
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3
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1.2k
views
CluserProfiler message "No gene can be mapped"
clusterProfiler
updated 4 months ago by 68k • written 4 months ago by • 0
0
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3
replies
1.2k
views
Gene Ontology (GO) Analysis
GOstats hyperGTest GO enrichGO clusterProfiler
4 months ago GA ▴ 10
0
votes
1
reply
465
views
Error in cnetplot
enrichplot clusterProfiler
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
0
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1
reply
682
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
7 months ago Jessica • 0
0
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4
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883
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
7 months ago Quang NN ▴ 10
2
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2
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833
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 10 months ago by ★ 1.2k • written 10 months ago by • 0
7
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9
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1.8k
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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 12 months ago by ★ 4.1k • written 12 months ago by • 0
0
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5
replies
1.3k
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 11 months ago by ▴ 760 • written 12 months ago by • 0
1
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2
replies
3.0k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 12 months ago by • 0
0
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1
reply
1.2k
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
1
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5
replies
2.1k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 13 months ago by • 0
2
votes
4
replies
1.4k
views
# Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.
clusterProfiler makeOrgPackage gseGO
updated 12 months ago by 68k • written 13 months ago by • 0
1
vote
2
replies
803
views
Question on number of genes used in GO analysis
GO clusterProfiler
13 months ago Danté • 0
1
vote
1
reply
1.2k
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis clusterProfiler viewPathway gsePathway
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
3
votes
1
reply
1.9k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 14 months ago by ★ 4.1k • written 14 months ago by ▴ 10
1
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2
replies
1.1k
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
15 months ago sawa • 0
1
vote
9
replies
3.0k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 15 months ago by 68k • written 15 months ago by ▴ 10
0
votes
1
reply
786
views
How can I get gseGO to return all GO terms tested?
clusterProfiler clusterp
updated 15 months ago by 68k • written 15 months ago by • 0
8
votes
6
replies
8.6k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
updated 15 months ago by ▴ 30 • written 6.4 years ago by ▴ 180
0
votes
4
replies
1.3k
views
error running enricher from clusterprofiler
clusterProfiler cluster
16 months ago Yael • 0
0
votes
1
reply
1.3k
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
1
vote
1
reply
661
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 16 months ago by 68k • written 16 months ago by ▴ 30
5
votes
13
replies
3.7k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
17 months ago • updated 16 months ago fernanda.backsouza ▴ 30
2
votes
2
replies
1.4k
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 17 months ago by 68k • written 17 months ago by • 0
1
vote
2
replies
2.4k
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
17 months ago Ana • 0
2
votes
4
replies
2.1k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 17 months ago by • 0
0
votes
2
replies
2.5k
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 23 days ago by • 0 • written 17 months ago by • 0
0
votes
1
reply
562
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 17 months ago by 68k • written 17 months ago by • 0
0
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0
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637
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
17 months ago andromeda • 0
2
votes
2
replies
1.3k
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 18 months ago by ▴ 10
4
votes
4
replies
5.1k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 18 months ago by • 0 • written 7.8 years ago by ▴ 20
2
votes
2
replies
1.7k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
18 months ago Eva ▴ 10
3
votes
9
replies
7.6k
views
enrichGOgradient color change
clusterProfiler
updated 8 months ago by • 0 • written 22 months ago by • 0
1
vote
1
reply
654
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 19 months ago by 68k • written 19 months ago by • 0
2
votes
15
replies
2.4k
views
Problems with enrichGO
clusterProfiler enrichGO
updated 19 months ago by 43k • written 19 months ago by • 0
0
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3
replies
1.5k
views
Unable to install clusterProfiler
clusterProfiler
updated 19 months ago by • 0 • written 19 months ago by • 0
0
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2
replies
1.3k
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
19 months ago mello-vieira • 0
0
votes
1
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1.3k
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 19 months ago by 68k • written 19 months ago by • 0
4
votes
2
replies
1.2k
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 20 months ago by ★ 4.1k • written 20 months ago by • 0
0
votes
3
replies
2.3k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 21 months ago by ★ 4.1k • written 21 months ago by • 0
3
votes
6
replies
4.2k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 21 months ago by 68k • written 2.9 years ago by ▴ 10
0
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9
replies
1.9k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
21 months ago nromerov • 0
2
votes
9
replies
3.4k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 22 months ago by ▴ 50 • written 22 months ago by ▴ 30
3
votes
4
replies
2.8k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 22 months ago by ★ 4.1k • written 22 months ago by • 0
0
votes
2
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1.0k
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
23 months ago georgii.vdovin • 0
0
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0
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837
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
23 months ago nromerov • 0
0
votes
2
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2.1k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 23 months ago by 68k • written 23 months ago by • 0
1
vote
2
replies
2.1k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
2.0 years ago fluentin44 • 0
0
votes
2
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3.3k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
2.1 years ago • updated 2.0 years ago Valéria • 0
288 results • Page 1 of 6
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Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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