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Showing :
clusterprofiler
•
reset
2
votes
2
replies
109
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
1 day ago • updated 20 hours ago
Eva
▴ 10
1
vote
7
replies
1.0k
views
enrichGOgradient color change
clusterProfiler
updated 1 day ago by
Guido Hooiveld
★ 3.9k • written 4 months ago by
inna.gur
• 0
1
vote
1
reply
145
views
Clsuter Profiler "counts"
enrich
clusterProfiler
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
mpluchs
• 0
2
votes
15
replies
502
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
cinzia.spagnoli
• 0
0
votes
3
replies
265
views
Unable to install clusterProfiler
clusterProfiler
updated 4 weeks ago by
Perry
• 0 • written 5 weeks ago by
harsh
• 0
0
votes
2
replies
223
views
Problem with buildGOmap from clusterProfiler
clusterProfiler
6 weeks ago
mello-vieira
• 0
0
votes
1
reply
178
views
ClusterProfiler result question: Why are all many of my resulting p.adjust values the same???
clusterProfiler
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
Max
• 0
4
votes
2
replies
262
views
Enrichement with clusterProfiler and biomart
biomaRt
clusterProfiler
Zea_mays
updated 8 weeks ago by
Guido Hooiveld
★ 3.9k • written 8 weeks ago by
sanchezsanchez
• 0
0
votes
3
replies
584
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 3 months ago by
Aastha Kapoor
• 0
3
votes
6
replies
1.9k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 3 months ago by
James W. MacDonald
65k • written 17 months ago by
Susanne
▴ 10
0
votes
9
replies
503
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
3 months ago
nromerov
• 0
2
votes
9
replies
1.0k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler
HPO.db
updated 4 months ago by
Erqiang Hu
▴ 50 • written 4 months ago by
jovel_juan
▴ 30
3
votes
4
replies
1.0k
views
Annotation hub and clusterProfiler errors
clusterProfiler
Annotationhub
updated 4 months ago by
Guido Hooiveld
★ 3.9k • written 4 months ago by
BS
• 0
0
votes
2
replies
392
views
Differential Expression Cutoffs for n = 1
clusterProfiler
DESeq2
5 months ago
georgii.vdovin
• 0
0
votes
0
replies
290
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler
DifferentialExpression
5 months ago
nromerov
• 0
0
votes
2
replies
533
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor
clusterProfiler
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
nilanjanamani88
• 0
1
vote
2
replies
691
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler
emapplot
6 months ago
fluentin44
• 0
0
votes
2
replies
923
views
apply clusterProfiler::simplify on merge_result list
clusterProfiler
6 months ago
Valéria
• 0
3
votes
2
replies
922
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 7 months ago by
Guido Hooiveld
★ 3.9k • written 7 months ago by
Milan
▴ 10
0
votes
3
replies
1.1k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot
GSEA
clusterProfiler
updated 4 months ago by
Fatemeh
• 0 • written 7 months ago by
Cen
• 0
0
votes
3
replies
1.3k
views
Not able to install clusterProfiler
clusterProfiler
updated 4 weeks ago by
Perry
• 0 • written 8 months ago by
Snehal
• 0
0
votes
0
replies
308
views
Downstream analysis of DEG for non-model organisms.
axolotl
KEGG
GOstats
clusterProfiler
8 months ago
georgii.vdovin
• 0
2
votes
5
replies
3.0k
views
How to use EnrichGo of Cluster Profiler
EnrichGO
clusterProfiler
written 3.2 years ago by
Carolina
• 0
0
votes
1
reply
643
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO
GeneSet
clusterProfiler
GeneSetEnrichment
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
manuelsokolov
• 0
0
votes
5
replies
905
views
plot enrichment results
enrichplot
clusterProfiler
updated 8 months ago by
Lluís Revilla Sancho
▴ 730 • written 8 months ago by
Manuela
• 0
0
votes
2
replies
600
views
Question regarding FAQ
clusterProfiler
9 months ago
kl-fr
• 0
0
votes
0
replies
708
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
9 months ago
pg45863
▴ 10
2
votes
4
replies
1.2k
views
Change dotsize to be the same in multiple plots - enrichplot dotplot
enrichplot
clusterProfiler
9 months ago
Tyroone
• 0
0
votes
1
reply
860
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler
AnnotationForge
updated 11 months ago by
shepherl
3.8k • written 11 months ago by
yuwt8920
• 0
0
votes
5
replies
1.2k
views
enrichKEGG function error
cluster
clusterProfiler
KEGG
11 months ago • updated 10 months ago
ruba-mahmoud
• 0
1
vote
3
replies
995
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG
clusterProfiler
Bioconductor
updated 11 months ago by
Guido Hooiveld
★ 3.9k • written 11 months ago by
m-bihie
▴ 10
0
votes
1
reply
541
views
what does "exp1" mean in the gage() function?
gage
clusterProfiler
DESeq2
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
m-bihie
▴ 10
0
votes
3
replies
3.3k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot
R
clusterProfiler
updated 12 months ago by
Guido Hooiveld
★ 3.9k • written 13 months ago by
YNKIM
• 0
0
votes
1
reply
1.1k
views
Am I able to add gene names/symbols to an enrichGO() output?
clusterProfiler
enrichplot
updated 12 months ago by
Guido Hooiveld
★ 3.9k • written 12 months ago by
GenoMexa
• 0
0
votes
1
reply
671
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 12 months ago by
ATpoint
★ 3.9k • written 12 months ago by
ruiqi.li
• 0
4
votes
2
replies
4.0k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG
clusterProfiler
updated 12 months ago by
Erqiang Hu
▴ 50 • written 12 months ago by
redafazazi
• 0
1
vote
7
replies
1.6k
views
Problem with universe argument in enrichKEGG
KEGG
clusterProfiler
keggorthology
updated 12 months ago by
Basti
▴ 750 • written 12 months ago by
ruiqi.li
• 0
2
votes
6
replies
1.8k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG
clusterProfiler
updated 10 weeks ago by
Guido Hooiveld
★ 3.9k • written 12 months ago by
ruiqi.li
• 0
0
votes
1
reply
604
views
Libraries loading error
DESeq2
clusterProfiler
enrichplot
updated 14 months ago by
Michael Love
41k • written 14 months ago by
joanna
• 0
0
votes
2
replies
1.8k
views
clusterProfiler - custom annotations
clusterProfiler
updated 10 weeks ago by
Guido Hooiveld
★ 3.9k • written 15 months ago by
adam
• 0
1
vote
1
reply
986
views
How to include background "universe" in compareCluster function of clusterprofiler package
clusterProfiler
updated 15 months ago by
Basti
▴ 750 • written 15 months ago by
ghs101
• 0
1
vote
7
replies
1.4k
views
Adding geneID to list of gene locus IDs
cluster
OrgDb
clusterProfiler
written 16 months ago by
Chruut
• 0
2
votes
4
replies
2.0k
views
question regarding installation of "enrichplot" with BiocManager
R
BiocManager
install
clusterProfiler
GO
written 15 months ago by
abhisek001
• 0
7
votes
6
replies
1.9k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 14 months ago by
Gordon Smyth
50k • written 15 months ago by
nhaus
▴ 10
0
votes
2
replies
3.4k
views
Error in UseMethod("rescale")
clusterProfiler
updated 15 months ago by
Guido Hooiveld
★ 3.9k • written 15 months ago by
vvelagal
• 0
0
votes
7
replies
2.8k
views
Mouse GSEA Analysis
clusterProfiler
updated 15 months ago by
Michael Love
41k • written 16 months ago by
Rob
• 0
0
votes
0
replies
789
views
Extracting gene lists per timepoints using DEGPPatterns package and LRT
DEGseq
clusterProfiler
DEGreport
16 months ago
Rob
• 0
1
vote
9
replies
1.4k
views
Why is OrgDb linked to specific biocversion? / How to analyze old datasets?
BiocVersion
OrgDb
clusterProfiler
16 months ago
MK
• 0
0
votes
0
replies
561
views
How to perform a cluster analysis in RT-qPCR or HT-qPCR results?
cluster
qpcr
qpcrNorm
clusterProfiler
HTqPCR
16 months ago
Javier
• 0
1
vote
0
replies
549
views
Over Representation Analysis using PFAM/InterPro database
PFAM.db
clusterProfiler
16 months ago
alexandr.gopanenko
▴ 50
50 results • Page
1 of 1
Recent ...
Replies
Comment: DEG Filtering
by
Amit
• 0
Hello Gordon, The PCA plot for RMA normalized data shows Mixing of samples. Is it Batch Effect ? Because when I apply ARSyNseq() and again …
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
James W. MacDonald
65k
Let's take a closer look. ``` > library(GEOquery) ## some random data > getGEOSuppFiles("GSE193983") > setwd("GSE193983/") > untar("GSE19…
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Votes
Comment: DEG Filtering
Answer: DEG Filtering
Answer: DEG Filtering
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
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