Showing : clusterProfiler • reset
1
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41
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OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 10 hours ago by ★ 3.9k • written 11 hours ago by • 0
1
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2
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76
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geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
2 days ago Ana • 0
2
votes
2
replies
148
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
6 days ago julia_mcdonough • 0
0
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1
reply
110
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 4 days ago by ★ 3.9k • written 8 days ago by • 0
0
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1
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146
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 10 days ago by 65k • written 11 days ago by • 0
0
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0
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122
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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
13 days ago andromeda • 0
2
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1
reply
175
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Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 25 days ago by ★ 3.9k • written 27 days 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 29 days ago by • 0 • written 6.3 years ago by ▴ 20
2
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2
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231
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
4 weeks ago Eva ▴ 10
1
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7
replies
1.3k
views
enrichGOgradient color change
clusterProfiler
updated 4 weeks ago by ★ 3.9k • written 5 months ago by • 0
1
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1
reply
173
views
Clsuter Profiler "counts"
enrich clusterProfiler
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
2
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15
replies
631
views
Problems with enrichGO
clusterProfiler enrichGO
updated 9 weeks ago by 41k • written 10 weeks ago by • 0
0
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3
replies
376
views
Unable to install clusterProfiler
clusterProfiler
updated 9 weeks ago by • 0 • written 10 weeks ago by • 0
0
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2
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287
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
10 weeks ago mello-vieira • 0
0
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1
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249
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
4
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2
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333
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 3 months ago by ★ 3.9k • written 3 months ago by • 0
0
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3
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756
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 4 months ago by ★ 3.9k • written 4 months ago by • 0
3
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6
replies
2.0k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 4 months ago by 65k • written 18 months ago by ▴ 10
0
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9
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602
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
4 months ago nromerov • 0
2
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9
replies
1.1k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 5 months ago by ▴ 50 • written 5 months ago by ▴ 30
3
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4
replies
1.1k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 5 months ago by ★ 3.9k • written 5 months ago by • 0
0
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2
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447
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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341
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
6 months ago nromerov • 0
0
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2
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603
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 6 months ago by 65k • written 6 months ago by • 0
1
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2
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808
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler emapplot
7 months ago fluentin44 • 0
0
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2
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1.1k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
7 months ago Valéria • 0
3
votes
2
replies
1.0k
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
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3
replies
1.2k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 5 months ago by • 0 • written 8 months ago by • 0
0
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3
replies
1.4k
views
Not able to install clusterProfiler
clusterProfiler
updated 9 weeks ago by • 0 • written 9 months ago by • 0
0
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0
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336
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
9 months ago georgii.vdovin • 0
2
votes
5
replies
3.1k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.3 years ago by • 0
0
votes
1
reply
746
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
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983
views
plot enrichment results
enrichplot clusterProfiler
updated 9 months ago by ▴ 730 • written 9 months ago by • 0
0
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2
replies
654
views
Question regarding FAQ
clusterProfiler
10 months ago kl-fr • 0
0
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0
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803
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
10 months ago pg45863 ▴ 10
2
votes
4
replies
1.4k
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot clusterProfiler
10 months ago Tyroone • 0
0
votes
1
reply
999
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 12 months ago by 3.8k • written 12 months ago by • 0
0
votes
5
replies
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 12 months ago by ★ 3.9k • written 12 months ago by ▴ 10
0
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1
reply
585
views
what does "exp1" mean in the gage() function?
gage clusterProfiler DESeq2
updated 12 months ago by 65k • written 12 months ago by ▴ 10
0
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3
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3.7k
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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2
replies
745
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 13 hours ago by • 0 • written 13 months ago by ▴ 10
4
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2
replies
4.3k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 13 months ago by ▴ 50 • written 13 months ago by • 0
1
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7
replies
1.8k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 13 months ago by ▴ 770 • written 13 months ago by ▴ 10
2
votes
6
replies
1.9k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 3 months ago by ★ 3.9k • written 13 months ago by ▴ 10
0
votes
1
reply
643
views
Libraries loading error
DESeq2 clusterProfiler enrichplot
updated 15 months ago by 41k • written 15 months ago by • 0
0
votes
2
replies
2.0k
views
clusterProfiler - custom annotations
clusterProfiler
updated 3 months ago by ★ 3.9k • written 16 months ago by • 0
1
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1
reply
1.1k
views
How to include background "universe" in compareCluster function of clusterprofiler package
clusterProfiler
updated 16 months ago by ▴ 770 • written 16 months ago by • 0
1
vote
7
replies
1.4k
views
Adding geneID to list of gene locus IDs
cluster OrgDb clusterProfiler
written 17 months ago by • 0
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Answer: How to make DGEList and design matrix by edgeR package by Gordon Smyth 50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Answer: Finding DEGs by using edgeR by Gordon Smyth 50k
I am not clear what you mean that you have already normalized your data. How exactly did you normalize the data? The best way to do an edg…
Answer: Log-cpm values from limma by Gordon Smyth 50k
The log-cpm values from voom() are not free of batch effect. If you want batch-corrected log-cpm values, we recommend cpm() followed by rem…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
As expected normalization is **way** off, meaning in simple terms that the cloud is too high. The deep-blue area should be along y=0. Try t…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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