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ClusterProfiler
•
reset
0
votes
4
replies
2.7k
views
How to use clusterProfiler to do GO enrichment analysis with unsupported organisms
clusterprofiler
go
Gff2GeneTable
buildgo
unsupported organisms
8.9 years ago
Didi
▴ 10
2
votes
4
replies
3.2k
views
Problem with BuildGOmap() in clusterProfiler
clusterprofiler
8.9 years ago
Marcus
• 0
1
vote
10
replies
5.2k
views
Issue of clusterprofiler package
clusterprofiler
updated 8.9 years ago by
Guangchuang Yu
★ 1.2k • written 8.9 years ago by
unique379
• 0
1
vote
5
replies
3.7k
views
clusterProfiler - get symbol from GSEA results
clusterProfiler
updated 8.9 years ago by
Guangchuang Yu
★ 1.2k • written 8.9 years ago by
Jane Merlevede
▴ 90
3
votes
7
replies
5.3k
views
clusterProfiler - GeneRatio & nb of genes always positively correlated in dotplot
clusterProfiler
8.9 years ago
Jane Merlevede
▴ 90
1
vote
2
replies
3.6k
views
clusterProfiler - difference in the number of genes from input and enrichGO results
clusterProfiler
updated 8.9 years ago by
Guangchuang Yu
★ 1.2k • written 8.9 years ago by
Jane Merlevede
▴ 90
0
votes
2
replies
4.6k
views
clusterProfiler - qvalue adjustment method in enricher()
clusterProfiler
updated 8.9 years ago by
Guangchuang Yu
★ 1.2k • written 8.9 years ago by
Jane Merlevede
▴ 90
0
votes
2
replies
3.0k
views
clusterProfiler - interpretation of plotGOgraph
clusterprofiler
topgo
8.9 years ago
Jane Merlevede
▴ 90
0
votes
3
replies
9.2k
views
clusterProfiler - how does showCategory work in dotplot from compareClusterResult class?
clusterprofiler
8.9 years ago
Jane Merlevede
▴ 90
1
vote
2
replies
6.3k
views
clusterProfiler : How works the q-value filtering ? What is a good cutoff ? Is this like an FDR ?
clusterprofiler
qvalue
updated 9.0 years ago by
Guangchuang Yu
★ 1.2k • written 9.0 years ago by
ZheFrench
▴ 60
0
votes
5
replies
3.3k
views
Questions on using clusterProfiler
clustering
clusterprofiler
9.0 years ago
zhangducsu
• 0
2
votes
6
replies
4.4k
views
leading edge analysis clusterProfiler DOSE custom GSEA
clusterprofiler
DOSE
GSEA_internal
USER_DATA
leading edge Analysis
9.0 years ago
Riba Michela
▴ 90
1
vote
2
replies
2.3k
views
can KEGG figures produced by pathview be used in publication, or that they are copyrighted ?
pathview
clusterprofiler
9.0 years ago
assaf www
▴ 140
0
votes
1
reply
1.2k
views
how to classify geneID in the compareCluster
clusterprofiler
updated 9.1 years ago by
Guangchuang Yu
★ 1.2k • written 9.1 years ago by
joseph
▴ 50
0
votes
1
reply
1.3k
views
input data format for enricher() function
clusterProfiler
9.1 years ago
joseph
▴ 50
0
votes
1
reply
1.9k
views
Add title to enrichMap and cnetplot plots
clusterprofiler
updated 9.1 years ago by
Guangchuang Yu
★ 1.2k • written 9.1 years ago by
David
▴ 860
0
votes
2
replies
2.1k
views
Returning less assigned genes than expected
clusterprofiler
9.2 years ago
David
▴ 860
0
votes
1
reply
3.3k
views
ClusterProfiler can't load gmt file
GSEA
clusterprofiler
gmt
updated 9.2 years ago by
Guangchuang Yu
★ 1.2k • written 9.2 years ago by
sarah.blackstone7734
• 0
0
votes
1
reply
1.2k
views
plot cannot presented for the clusterprofiler results
clusterprofiler
updated 9.2 years ago by
Guangchuang Yu
★ 1.2k • written 9.2 years ago by
joseph
▴ 50
1
vote
2
replies
1.8k
views
clusterProfiler: enrichDavid produces NA values
clusterProfiler
9.2 years ago
n.kreim
▴ 20
2
votes
2
replies
5.0k
views
Bgratio column in clusterProfiler enrichGO results
clusterprofiler
updated 2.2 years ago by
Trinh
• 0 • written 9.3 years ago by
mdtorohernando
▴ 10
0
votes
1
reply
3.7k
views
Combining compareCluster with enricher in clusterProfiler
clusterprofiler
updated 9.3 years ago by
Guangchuang Yu
★ 1.2k • written 9.3 years ago by
JD
▴ 10
6
votes
2
replies
5.8k
views
help with clusterProfiler enricher function
clusterprofiler
9.5 years ago • updated 9.4 years ago
naholi.alejandri
▴ 50
1
vote
4
replies
3.8k
views
Problem retrieving graphics in clusterprofiler
software error
clusterprofiler
GO
genesetenrichment
9.4 years ago
José Luis Lavín
▴ 10
4
votes
10
replies
8.3k
views
Help with enrichKEGG function in clusterProfiler
clusterprofiler
updated 3.2 years ago by
Nitish Kumar Mishra
▴ 40 • written 9.7 years ago by
1992
▴ 10
0
votes
0
replies
3.4k
views
Modifying the legend in cnetplot function
clusterProfiler
DOSE
9.9 years ago
Vinicius Henrique da Silva
▴ 40
0
votes
2
replies
2.5k
views
library(clusterProfiler) cnetplot(fixed = F): why can´t I get the color legend?
clusterprofiler
tkplot
9.9 years ago
cristina della beffa
▴ 30
3
votes
5
replies
3.0k
views
Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
pathview
clusterProfiler
KEGGpath
visualization
Graphviz
updated 9.9 years ago by
Luo Weijun
★ 1.6k • written 9.9 years ago by
svlachavas
▴ 840
1
vote
1
reply
1.9k
views
KEGGREST fail to fetch human genes link to pathway
keggrest
clusterProfiler
updated 10.1 years ago by
Dan Tenenbaum
★ 8.2k • written 10.1 years ago by
Guangchuang Yu
★ 1.2k
0
votes
2
replies
1.5k
views
GO annotation missing in org.EcSakai.eg.db?
org.EcSakai.eg.db
Annotation
go
clusterProfiler
updated 10.2 years ago by
James W. MacDonald
68k • written 10.2 years ago by
Guangchuang Yu
★ 1.2k
0
votes
3
replies
2.7k
views
enrichGO() for unsupported organisms - library(clusterProfiler)
clusterProfiler
go
annotation
10.3 years ago
cristina della beffa
▴ 30
1
vote
2
replies
3.6k
views
cnetplot() - library(clusterProfiler)
clusterProfiler
network
10.3 years ago
cristina della beffa
▴ 30
1
vote
3
replies
2.0k
views
buildKEGGmap doesn´t work - library(clusterProfiler)
clusterprofiler
software error
updated 10.4 years ago by
Guangchuang Yu
★ 1.2k • written 10.4 years ago by
cristina della beffa
▴ 30
1
vote
4
replies
5.9k
views
ClusterProfiler: enrichGO / compareCluster and Pvalue threeshold
clusterprofiler
updated 10.5 years ago by
Guangchuang Yu
★ 1.2k • written 10.5 years ago by
samuel collombet
▴ 140
1
vote
5
replies
2.8k
views
About the state of KEGG-related packages
KEGGSOAP
KEGGgraph
keggorthology
clusterProfiler
KEGGprofile
PathNet
KEGGSOAP
KEGGgraph
updated 12.2 years ago by
Luo Weijun
★ 1.6k • written 12.2 years ago by
enricoferrero
▴ 680
0
votes
0
replies
1.7k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO
Cancer
Rgraphviz
clusterProfiler
DOSE
GO
Cancer
Rgraphviz
clusterProfiler
DOSE
12.3 years ago
Martin Morgan
25k
0
votes
3
replies
2.4k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO
clusterProfiler
DOSE
GO
clusterProfiler
DOSE
updated 12.3 years ago by
Dan Tenenbaum
★ 8.2k • written 12.3 years ago by
Guest User
★ 13k
0
votes
0
replies
1.1k
views
xzfile() cannot open the connection, lzma encoder error 5.
clusterProfiler
clusterProfiler
12.3 years ago
Jose Guillen
▴ 10
288 results • Page
6 of 6
Recent ...
Replies
Comment: Help with defining groups
by
Phinney, Brett
▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness
by
massimo
• 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package
by
ksankaran
• 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
by
ATpoint
★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes
by
ATpoint
★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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