Showing : clusterprofiler • reset
1
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1
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106
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 10 days ago by 65k • written 10 days ago by ▴ 10
1
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13
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382
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Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
12 days ago • updated 9 days ago fernanda.backsouza ▴ 10
2
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2
replies
183
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OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 14 days ago by 65k • written 15 days ago by • 0
1
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2
replies
133
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geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
17 days ago Ana • 0
2
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2
replies
189
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
21 days ago julia_mcdonough • 0
0
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1
reply
157
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 19 days ago by ★ 3.9k • written 23 days ago by • 0
0
votes
1
reply
178
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 25 days ago by 65k • written 26 days ago by • 0
0
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0
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143
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Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
28 days ago andromeda • 0
2
votes
1
reply
211
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 5 weeks ago by ★ 3.9k • written 6 weeks ago by ▴ 10
4
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4
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3.7k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 6 weeks ago by • 0 • written 6.4 years ago by ▴ 20
2
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2
replies
258
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
6 weeks ago Eva ▴ 10
1
vote
7
replies
1.5k
views
enrichGOgradient color change
clusterProfiler
updated 6 weeks ago by ★ 3.9k • written 5 months ago by • 0
1
vote
1
reply
198
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
2
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15
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692
views
Problems with enrichGO
clusterProfiler enrichGO
updated 11 weeks ago by 41k • written 12 weeks ago by • 0
0
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3
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417
views
Unable to install clusterProfiler
clusterProfiler
updated 11 weeks ago by • 0 • written 12 weeks ago by • 0
0
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2
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317
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
3 months ago • updated 12 weeks ago mello-vieira • 0
0
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1
reply
272
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 3 months ago by 65k • written 3 months ago by • 0
4
votes
2
replies
363
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 3 months ago by ★ 3.9k • written 3 months ago by • 0
0
votes
3
replies
814
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 5 months ago by ★ 3.9k • written 5 months ago by • 0
3
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6
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2.1k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 5 months ago by 65k • written 18 months ago by ▴ 10
0
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9
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658
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
5 months ago nromerov • 0
2
votes
9
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1.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 6 months ago by ▴ 50 • written 6 months ago by ▴ 30
3
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4
replies
1.2k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 6 months ago by ★ 3.9k • written 6 months ago by • 0
0
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2
replies
470
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
6 months ago georgii.vdovin • 0
0
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0
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365
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
6 months ago nromerov • 0
0
votes
2
replies
645
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 7 months ago by 65k • written 7 months ago by • 0
1
vote
2
replies
860
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
7 months ago fluentin44 • 0
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2
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1.2k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
8 months ago Valéria • 0
3
votes
2
replies
1.1k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 8 months ago by ★ 3.9k • written 8 months ago by ▴ 10
0
votes
3
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1.3k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 6 months ago by • 0 • written 8 months ago by • 0
0
votes
3
replies
1.5k
views
Not able to install clusterProfiler
clusterProfiler
updated 11 weeks ago by • 0 • written 9 months ago by • 0
0
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0
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352
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
9 months ago georgii.vdovin • 0
2
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5
replies
3.2k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.3 years ago by • 0
0
votes
1
reply
807
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO GeneSet clusterProfiler GeneSetEnrichment
updated 9 months ago by 65k • written 9 months ago by • 0
0
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5
replies
1.0k
views
plot enrichment results
enrichplot clusterProfiler
updated 10 months ago by ▴ 730 • written 10 months ago by • 0
0
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2
replies
689
views
Question regarding FAQ
clusterProfiler
10 months ago kl-fr • 0
0
votes
0
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834
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
11 months ago pg45863 ▴ 10
2
votes
4
replies
1.5k
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot clusterProfiler
11 months ago Tyroone • 0
0
votes
1
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1.1k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 12 months ago by 3.9k • written 12 months ago by • 0
0
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5
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1.3k
views
enrichKEGG function error
cluster clusterProfiler KEGG
12 months ago • updated 11 months ago ruba-mahmoud • 0
1
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3
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1.1k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 13 months ago by ★ 3.9k • written 13 months ago by ▴ 10
0
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1
reply
597
views
what does "exp1" mean in the gage() function?
gage clusterProfiler DESeq2
updated 13 months ago by 65k • written 13 months ago by ▴ 10
0
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3
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3.8k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 13 months ago by ★ 3.9k • written 14 months ago by • 0
0
votes
1
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1.2k
views
Am I able to add gene names/symbols to an enrichGO() output?
clusterProfiler enrichplot
updated 13 months ago by ★ 3.9k • written 13 months ago by • 0
1
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3
replies
854
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 9 days ago by ★ 1.2k • written 14 months ago by ▴ 10
4
votes
2
replies
4.4k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 14 months ago by ▴ 50 • written 14 months ago by • 0
1
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7
replies
1.8k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 14 months ago by ▴ 780 • written 14 months ago by ▴ 10
2
votes
6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 3 months ago by ★ 3.9k • written 14 months ago by ▴ 10
0
votes
1
reply
659
views
Libraries loading error
DESeq2 clusterProfiler enrichplot
updated 15 months ago by 41k • written 15 months ago by • 0
0
votes
2
replies
2.1k
views
clusterProfiler - custom annotations
clusterProfiler
updated 3 months ago by ★ 3.9k • written 16 months ago by • 0
50 results • Page 1 of 1
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Votes
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
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