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clusterProfiler
•
reset
0
votes
1
reply
123
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler
KEGG
9 days ago
Jessica
• 0
0
votes
4
replies
457
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2
GSEA
clusterProfiler
4 weeks ago
Quang NN
▴ 10
2
votes
2
replies
534
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 3 months ago by
Guangchuang Yu
★ 1.2k • written 4 months ago by
Asma
• 0
7
votes
9
replies
1.3k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO
clusterProfiler
enr
updated 5 months ago by
Guido Hooiveld
★ 4.1k • written 5 months ago by
Fatima
• 0
0
votes
5
replies
887
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor
clusterProfiler
updated 5 months ago by
Lluís Revilla Sancho
▴ 760 • written 5 months ago by
semra
• 0
1
vote
2
replies
1.7k
views
How to use compareCluster in ClusterProfiler?
RNASeqData
GSEA
clusterProfiler
written 5 months ago by
b8177
• 0
0
votes
1
reply
708
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 5 months ago by
Guido Hooiveld
★ 4.1k • written 5 months ago by
sherinesaber
• 0
1
vote
5
replies
1.4k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler
heatmaps
written 6 months ago by
Claudio
• 0
2
votes
4
replies
972
views
# Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.
clusterProfiler
makeOrgPackage
gseGO
updated 5 months ago by
James W. MacDonald
68k • written 6 months ago by
Nuria Mauri
• 0
1
vote
2
replies
492
views
Question on number of genes used in GO analysis
GO
clusterProfiler
6 months ago
Danté
• 0
1
vote
1
reply
719
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis
clusterProfiler
viewPathway
gsePathway
updated 7 months ago by
Guido Hooiveld
★ 4.1k • written 7 months ago by
Filipe
• 0
3
votes
1
reply
1.3k
views
Difference between enrichGO results and Enrichr website results
Pathways
GO.db
clusterProfiler
updated 7 months ago by
Guido Hooiveld
★ 4.1k • written 7 months ago by
adrip
▴ 10
1
vote
2
replies
808
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
8 months ago
sawa
• 0
1
vote
9
replies
1.9k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2
clusterProfiler
Pathways
RNASeq
org.Mm.eg.db
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
adrip
▴ 10
0
votes
1
reply
533
views
How can I get gseGO to return all GO terms tested?
clusterProfiler
clusterp
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
yesitsjess
• 0
8
votes
6
replies
6.8k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler
enrichplot
updated 9 months ago by
jovel_juan
▴ 30 • written 5.8 years ago by
charles.foster
▴ 160
0
votes
4
replies
826
views
error running enricher from clusterprofiler
clusterProfiler
cluster
9 months ago
Yael
• 0
0
votes
1
reply
911
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 9 months ago by
Guido Hooiveld
★ 4.1k • written 9 months ago by
aogunbaw
• 0
1
vote
1
reply
440
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 10 months ago by
James W. MacDonald
68k • written 10 months ago by
fernanda.backsouza
▴ 30
5
votes
13
replies
2.6k
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
10 months ago
fernanda.backsouza
▴ 30
2
votes
2
replies
936
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 10 months ago by
James W. MacDonald
68k • written 10 months ago by
sansan
• 0
1
vote
2
replies
1.5k
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
10 months ago
Ana
• 0
2
votes
3
replies
1.1k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
updated 3 months ago by
josephasmith1310
• 0 • written 10 months ago by
julia_mcdonough
• 0
0
votes
1
reply
1.6k
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 10 months ago by
Guido Hooiveld
★ 4.1k • written 10 months ago by
Lucie
• 0
0
votes
1
reply
443
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 10 months ago by
James W. MacDonald
68k • written 10 months ago by
BCS12
• 0
0
votes
0
replies
478
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
10 months ago
andromeda
• 0
2
votes
2
replies
954
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
written 11 months ago by
enee
▴ 10
4
votes
4
replies
4.6k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 11 months ago by
jandrade
• 0 • written 7.2 years ago by
Huang, Lei [BSD] - CRI
▴ 20
2
votes
2
replies
1.1k
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
11 months ago
Eva
▴ 10
3
votes
9
replies
5.4k
views
enrichGOgradient color change
clusterProfiler
updated 7 weeks ago by
lewis.roper
• 0 • written 15 months ago by
inna.gur
• 0
1
vote
1
reply
490
views
Clsuter Profiler "counts"
enrich
clusterProfiler
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
mpluchs
• 0
2
votes
15
replies
1.7k
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 12 months ago by
Michael Love
43k • written 12 months ago by
cinzia.spagnoli
• 0
0
votes
3
replies
1.2k
views
Unable to install clusterProfiler
clusterProfiler
updated 12 months ago by
Perry
• 0 • written 12 months ago by
harsh
• 0
0
votes
2
replies
964
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
12 months ago
mello-vieira
• 0
0
votes
1
reply
931
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
Max
• 0
4
votes
2
replies
920
views
Enrichement with clusterProfiler and biomart
biomaRt
clusterProfiler
Zea_mays
updated 13 months ago by
Guido Hooiveld
★ 4.1k • written 13 months ago by
sansan
• 0
0
votes
3
replies
1.9k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 14 months ago by
Guido Hooiveld
★ 4.1k • written 14 months ago by
Aastha Kapoor
• 0
3
votes
6
replies
3.5k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 15 months ago by
James W. MacDonald
68k • written 2.3 years ago by
Susanne
▴ 10
0
votes
9
replies
1.4k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
15 months ago
nromerov
• 0
2
votes
9
replies
3.0k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler
HPO.db
updated 16 months ago by
Erqiang Hu
▴ 50 • written 16 months ago by
jovel_juan
▴ 30
3
votes
4
replies
2.1k
views
Annotation hub and clusterProfiler errors
clusterProfiler
Annotationhub
updated 16 months ago by
Guido Hooiveld
★ 4.1k • written 16 months ago by
BS
• 0
0
votes
2
replies
851
views
Differential Expression Cutoffs for n = 1
clusterProfiler
DESeq2
16 months ago
georgii.vdovin
• 0
0
votes
0
replies
694
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler
DifferentialExpression
16 months ago
nromerov
• 0
0
votes
2
replies
1.6k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor
clusterProfiler
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
nilanjanamani88
• 0
1
vote
2
replies
1.6k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler
emapplot
17 months ago
fluentin44
• 0
0
votes
2
replies
2.5k
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
18 months ago • updated 17 months ago
Valéria
• 0
3
votes
2
replies
2.1k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 18 months ago by
Guido Hooiveld
★ 4.1k • written 18 months ago by
Milan
▴ 10
0
votes
3
replies
2.5k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot
GSEA
clusterProfiler
updated 16 months ago by
Fatemeh
• 0 • written 18 months ago by
Cen
• 0
0
votes
3
replies
2.9k
views
Not able to install clusterProfiler
clusterProfiler
updated 12 months ago by
Perry
• 0 • written 19 months ago by
Snehal
• 0
0
votes
0
replies
580
views
Downstream analysis of DEG for non-model organisms.
axolotl
KEGG
GOstats
clusterProfiler
19 months ago
georgii.vdovin
• 0
50 results • Page
1 of 1
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Comment: Differential variance analysis - can i use deseq2
by
Michael Love
43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis
by
Gordon Smyth
52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA
by
pammelala304
• 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get()
by
Matthew Thornton
▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data
by
user_bioinfo
• 0
yes actually that's why I did, and its all good! thank you for your response
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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