Showing : clusterProfiler • reset
2
votes
2
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418
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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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691
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
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1.1k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 3 months ago by • 0
0
votes
1
reply
516
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
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4
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825
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
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2
replies
401
views
Question on number of genes used in GO analysis
GO clusterProfiler
4 months ago Danté • 0
1
vote
1
reply
528
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
1.0k
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
vote
2
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697
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
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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
428
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 7 months ago by ▴ 30 • written 5.6 years ago by ▴ 160
0
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4
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655
views
error running enricher from clusterprofiler
clusterProfiler cluster
7 months ago Yael • 0
0
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1
reply
750
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
1
vote
1
reply
379
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 8 months ago by 67k • written 8 months ago by ▴ 30
5
votes
13
replies
2.2k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
8 months ago fernanda.backsouza ▴ 30
2
votes
2
replies
792
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
907
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
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1
reply
1.3k
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
395
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
427
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
783
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
935
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
9 months ago Eva ▴ 10
1
vote
8
replies
4.5k
views
enrichGOgradient color change
clusterProfiler
updated 7 months ago by • 0 • written 13 months ago by • 0
1
vote
1
reply
429
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
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3
replies
1.0k
views
Unable to install clusterProfiler
clusterProfiler
updated 10 months ago by • 0 • written 10 months ago by • 0
0
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2
replies
847
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
10 months ago mello-vieira • 0
0
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1
reply
768
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 11 months ago by 67k • written 11 months ago by • 0
4
votes
2
replies
833
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
1.8k
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
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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
13 months ago • updated 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 14 months ago by ▴ 30
3
votes
4
replies
1.9k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
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2
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787
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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621
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 15 months ago by 67k • written 15 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
votes
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
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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
replies
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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534
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
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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