Showing : ClusterProfiler • reset
2
votes
15
replies
695
views
Problems with enrichGO
clusterProfiler enrichGO
updated 11 weeks ago by 41k • written 12 weeks ago by • 0
0
votes
13
replies
2.9k
views
EnrichGO not working with db created from annotationhub
clusterProfiler AnnotationHubData GO
updated 23 months ago by ★ 3.9k • written 24 months ago by ▴ 10
1
vote
13
replies
14k
views
GeneList issue ClusterProfiler
genelist clusterprofiler
6.9 years ago bhgyu ▴ 30
1
vote
13
replies
389
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
12 days ago • updated 9 days ago fernanda.backsouza ▴ 10
5
votes
13
replies
4.2k
views
Getting error
enrichplot clusterProfiler org.Hs.eg.db
updated 2.1 years ago by ▴ 40 • written 2.1 years ago by • 0
3
votes
11
replies
5.0k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 12 weeks ago by ★ 3.9k • written 3.2 years ago by • 0
2
votes
11
replies
7.2k
views
ClusterProfiler enrichGO function leads to different enrichment results in different computers, while the code and gene list keep same
clusterProfiler
2.4 years ago liuzhy ▴ 10
6
votes
11
replies
7.8k
views
Cluster profiler - KEGG analysis
clusterprofiler
3.8 years ago sunnykevin97 • 0
4
votes
10
replies
6.2k
views
Help with enrichKEGG function in clusterProfiler
clusterprofiler
updated 21 months ago by ▴ 40 • written 8.2 years ago by ▴ 10
2
votes
10
replies
12k
views
keytype not supported in clusterprofiler when it is ensembl IDs?
clusterProfiler enrichGO
updated 4.0 years ago by 65k • written 4.0 years ago by ▴ 30
1
vote
10
replies
4.0k
views
Issue of clusterprofiler package
clusterprofiler
updated 7.5 years ago by ★ 1.2k • written 7.5 years ago by • 0
0
votes
9
replies
4.4k
views
What does "level" argument mean in groupGO function (cluster profiler)?
clusterprofiler go groupGO
updated 6.0 years ago by 65k • written 6.0 years ago by ▴ 360
1
vote
9
replies
3.0k
views
Dotplots for differential gene expression data ?
clusterprofiler
3.8 years ago sunnykevin97 • 0
0
votes
9
replies
659
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
5 months ago nromerov • 0
2
votes
9
replies
1.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 6 months ago by ▴ 50 • written 6 months ago by ▴ 30
0
votes
9
replies
2.8k
views
clusterProfiler setup specified order
clusterProfiler
7.0 years ago joseph ▴ 50
1
vote
9
replies
1.5k
views
Why is OrgDb linked to specific biocversion? / How to analyze old datasets?
BiocVersion OrgDb clusterProfiler
18 months ago MK • 0
8
votes
9
replies
8.9k
views
Error: package or namespace load failed for ‘clusterProfiler’: object ‘get_fun_from_pkg’ is not exported by 'namespace:rvcheck'
get_fun_from_pkg clusterProfiler rvcheck
updated 2.4 years ago by • 0 • written 2.6 years ago by • 0
2
votes
8
replies
1.7k
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error enrichGO annotationHub clusterProfiler Job
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
0
votes
8
replies
2.5k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
4.0 years ago felix.thaler • 0
0
votes
8
replies
2.7k
views
Got an confusing about BgRatio in enrichKEGG result of clusterprofiler
clusterprofiler
updated 7.4 years ago by ★ 1.2k • written 7.4 years ago by ▴ 30
1
vote
7
replies
1.8k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 14 months ago by ▴ 780 • written 14 months ago by ▴ 10
1
vote
7
replies
1.5k
views
Adding geneID to list of gene locus IDs
cluster OrgDb clusterProfiler
written 17 months ago by • 0
0
votes
7
replies
3.1k
views
Mouse GSEA Analysis
clusterProfiler
updated 17 months ago by 41k • written 18 months ago by • 0
3
votes
7
replies
4.5k
views
clusterProfiler - GeneRatio & nb of genes always positively correlated in dotplot
clusterProfiler
7.5 years ago Jane Merlevede ▴ 90
1
vote
7
replies
1.5k
views
enrichGOgradient color change
clusterProfiler
updated 6 weeks ago by ★ 3.9k • written 5 months ago by • 0
0
votes
6
replies
4.6k
views
enrichMKEGG can not identify the species
clusterprofiler
updated 5.8 years ago by ★ 3.9k • written 5.8 years ago by • 0
2
votes
6
replies
2.0k
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
votes
6
replies
3.5k
views
clusterProfiler: different runs return different results for gse functions
clusterprofiler
updated 3.0 years ago by ▴ 10 • written 6.7 years ago by • 0
0
votes
6
replies
8.7k
views
No gene can be mapped error with clusterprofiler
clusterprofiler r
updated 3 months ago by ★ 3.9k • written 7.3 years ago by • 0
4
votes
6
replies
3.7k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 20 months ago by ★ 3.9k • written 22 months ago by ▴ 10
7
votes
6
replies
2.1k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 16 months ago by 50k • written 17 months ago by ▴ 30
0
votes
6
replies
7.1k
views
question on GO analysis using clusterProfiler
clusterprofiler geneontology
updated 6.5 years ago by ▴ 160 • written 6.5 years ago by • 0
3
votes
6
replies
2.1k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 5 months ago by 65k • written 18 months ago by ▴ 10
2
votes
6
replies
12k
views
GSEA using clusterProfiler
GSEA clusterProfiler
6.5 years ago giuseppe0525 • 0
2
votes
6
replies
3.1k
views
leading edge analysis clusterProfiler DOSE custom GSEA
clusterprofiler DOSE GSEA_internal USER_DATA leading edge Analysis
7.6 years ago Riba Michela ▴ 90
1
vote
5
replies
1.1k
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
3.9 years ago Ruixuan ▴ 10
2
votes
5
replies
3.6k
views
GO enrichment comparison with other programs
clusterprofiler enrichment analysis
updated 7.3 years ago by ★ 1.2k • written 7.3 years ago by ▴ 30
0
votes
5
replies
4.3k
views
odd results "No enrichment found in any of gene cluster"
clusterprofiler
updated 6.9 years ago by ★ 1.2k • written 6.9 years ago by ▴ 50
3
votes
5
replies
2.0k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.1 years ago thomasjenner333 • 0
0
votes
5
replies
2.1k
views
Yeast org.Sc.sgd.db lacks SYMBOL - should it have one? - how to make it interoperate with clusterProfiler in its absence?
annotation go clusterProfiler org.Sc.sgd.db
5.2 years ago • updated 5.1 years ago Malcolm Cook ★ 1.6k
3
votes
5
replies
3.2k
views
how to color specific node or gene symbol from cnetplot ?
clusterProfiler enrichplot cnetplot GuangchuangYu
updated 20 months ago by ★ 1.2k • written 23 months ago by ▴ 30
1
vote
5
replies
2.7k
views
clusterProfiler - get symbol from GSEA results
clusterProfiler
updated 7.5 years ago by ★ 1.2k • written 7.5 years ago by ▴ 90
1
vote
5
replies
2.0k
views
About the state of KEGG-related packages
KEGGSOAP KEGGgraph keggorthology clusterProfiler KEGGprofile PathNet KEGGSOAP KEGGgraph
updated 10.8 years ago by ★ 1.6k • written 10.8 years ago by ▴ 660
0
votes
5
replies
1.8k
views
enrichGO returning NA
clusterprofiler org.hs.eg.db
updated 6.4 years ago by ★ 1.2k • written 6.4 years ago by • 0
0
votes
5
replies
9.3k
views
Cannot install clusterProfiler
clusterprofiler biocinstaller
updated 2.4 years ago by ▴ 10 • written 6.0 years ago by • 0
8
votes
5
replies
4.1k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler enrichplot
5.0 years ago • updated 23 months ago charles.foster ▴ 160
0
votes
5
replies
1.3k
views
enrichKEGG function error
cluster clusterProfiler KEGG
12 months ago • updated 11 months ago ruba-mahmoud • 0
0
votes
5
replies
1.0k
views
plot enrichment results
enrichplot clusterProfiler
updated 10 months ago by ▴ 730 • written 10 months ago by • 0
3
votes
5
replies
2.3k
views
Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
pathview clusterProfiler KEGGpath visualization Graphviz
updated 8.5 years ago by ★ 1.6k • written 8.5 years ago by ▴ 830
50 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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