Showing : clusterProfiler • reset
1
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58
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Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 2 days ago by 65k • written 2 days ago by ▴ 10
1
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13
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252
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Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
3 days ago • updated 20 hours ago fernanda.backsouza ▴ 10
2
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2
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139
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OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 6 days ago by 65k • written 6 days ago by • 0
1
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2
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111
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geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
9 days ago Ana • 0
2
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2
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167
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
13 days ago • updated 12 days ago julia_mcdonough • 0
0
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1
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133
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compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 11 days ago by ★ 3.9k • written 14 days ago by • 0
0
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1
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160
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How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 17 days ago by 65k • written 17 days ago by • 0
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0
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134
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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
20 days ago • updated 19 days ago andromeda • 0
2
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1
reply
188
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 4 weeks ago by ★ 3.9k • written 4 weeks ago by ▴ 10
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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 5 weeks ago by • 0 • written 6.4 years ago by ▴ 20
2
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2
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242
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padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot barplot clusterProfiler
5 weeks ago Eva ▴ 10
1
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7
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1.4k
views
enrichGOgradient color change
clusterProfiler
updated 5 weeks ago by ★ 3.9k • written 5 months ago by • 0
1
vote
1
reply
182
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Clsuter Profiler "counts"
enrich clusterProfiler
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
2
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15
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659
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Problems with enrichGO
clusterProfiler enrichGO
updated 10 weeks ago by 41k • written 11 weeks ago by • 0
0
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3
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382
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Unable to install clusterProfiler
clusterProfiler
updated 9 weeks ago by • 0 • written 11 weeks ago by • 0
0
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2
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297
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Problem with buildGOmap from clusterProfiler
clusterProfiler
11 weeks ago mello-vieira • 0
0
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1
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258
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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
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2
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344
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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779
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
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2.1k
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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624
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It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
5 months ago • updated 4 months ago nromerov • 0
2
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9
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1.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 5 months ago by ▴ 50 • written 6 months ago by ▴ 30
3
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4
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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
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452
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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350
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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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620
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
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2
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830
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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1.1k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
8 months ago • updated 7 months ago Valéria • 0
3
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2
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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
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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
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3
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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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340
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Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
9 months ago georgii.vdovin • 0
2
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5
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3.1k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.3 years ago by • 0
0
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1
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780
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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1.0k
views
plot enrichment results
enrichplot clusterProfiler
updated 9 months ago by ▴ 730 • written 10 months ago by • 0
0
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2
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672
views
Question regarding FAQ
clusterProfiler
10 months ago kl-fr • 0
0
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0
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817
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fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
11 months ago pg45863 ▴ 10
2
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4
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1.5k
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot clusterProfiler
11 months ago Tyroone • 0
0
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1
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1.0k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 12 months ago by 3.8k • written 12 months ago by • 0
0
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5
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1.3k
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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
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590
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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3.7k
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
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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
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811
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 1 day ago by ★ 1.2k • written 13 months ago by ▴ 10
4
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2
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4.3k
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
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1.8k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 13 months ago by ▴ 780 • written 14 months ago by ▴ 10
2
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6
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1.9k
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
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1
reply
653
views
Libraries loading error
DESeq2 clusterProfiler enrichplot
updated 15 months ago by 41k • written 15 months ago by • 0
0
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2
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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
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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