Showing : clusterProfiler • reset
0
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1
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149
views
Error in cnetplot
enrichplot clusterProfiler
updated 5 days ago by ★ 4.1k • written 11 days ago by • 0
0
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1
reply
223
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
6 weeks ago Jessica • 0
0
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4
replies
554
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
9 weeks ago Quang NN ▴ 10
2
votes
2
replies
619
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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1.4k
views
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
replies
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 6 months ago by • 0
0
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1
reply
845
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 6 months ago by ★ 4.1k • written 7 months ago by • 0
1
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5
replies
1.6k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 7 months ago by • 0
2
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4
replies
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
replies
576
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Question on number of genes used in GO analysis
GO clusterProfiler
7 months ago Danté • 0
1
vote
1
reply
878
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
vote
2
replies
888
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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2.2k
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
610
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
967
views
error running enricher from clusterprofiler
clusterProfiler cluster
10 months ago Yael • 0
0
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1
reply
1.0k
views
Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
1
vote
1
reply
466
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 11 months ago by 68k • written 11 months ago by ▴ 30
5
votes
13
replies
3.0k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
11 months ago fernanda.backsouza ▴ 30
2
votes
2
replies
1.0k
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
replies
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
reply
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
votes
1
reply
473
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 11 months ago by 68k • written 11 months ago by • 0
0
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0
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508
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
11 months ago andromeda • 0
2
votes
2
replies
1.1k
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 12 months ago by ▴ 10
4
votes
4
replies
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
votes
2
replies
1.3k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
12 months ago Eva ▴ 10
3
votes
9
replies
6.0k
views
enrichGOgradient color change
clusterProfiler
updated 12 weeks ago by • 0 • written 16 months ago by • 0
1
vote
1
reply
515
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
votes
3
replies
1.3k
views
Unable to install clusterProfiler
clusterProfiler
updated 13 months ago by • 0 • written 13 months ago by • 0
0
votes
2
replies
1.0k
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
14 months ago • updated 13 months ago mello-vieira • 0
0
votes
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
replies
980
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
votes
6
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3.6k
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
replies
1.6k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
16 months ago nromerov • 0
2
votes
9
replies
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
votes
4
replies
2.2k
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
replies
883
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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731
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
17 months ago nromerov • 0
0
votes
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
vote
2
replies
1.8k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
18 months ago fluentin44 • 0
0
votes
2
replies
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
votes
3
replies
2.6k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 17 months ago by • 0 • written 19 months ago by • 0
0
votes
3
replies
3.1k
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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Comment: Design Matrix with paired and independent samples plus RUVg Spike-in normalizati by Mei • 0
I have a similar experiment with 7 paired samples (T0 and T1) in each of 4 outcome groups. I am using RUVr combined with limma-voom, so I a…
Comment: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Arctic • 0
Many thanks for the link to the C++ code. I will see if I can find someone with C++ experience to help me with the code breakdown from her…
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Aaron Lun ★ 28k
It's calling C++ code, see the relevant function definitions on [GitHub](https://github.com/knncolle/BiocNeighbors/blob/master/src/generics…
Answer: DESeq2 by ATpoint ★ 4.8k
Time courses are often inevitable batches but you should have done the library prep at the same day, just extract RNA per day. If not then …
Comment: Package developing and interoperation with Bioconductor by slizchap • 0
Thank you so much for your answer. This was very useful, I will optimize my functions so they can handle SE objects.
Votes
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?
Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin
Comment: ComBat with repeated measures
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