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gostats
•
reset
0
votes
0
replies
354
views
Downstream analysis of DEG for non-model organisms.
axolotl
KEGG
GOstats
clusterProfiler
9 months ago
georgii.vdovin
• 0
0
votes
0
replies
393
views
plotGOTermGraph connects all subtrees to the root node
GO.db
GOstats
11 months ago
RuBBiT0
▴ 10
1
vote
9
replies
1.2k
views
GOstats - subsetting termGraphs with terms from the html report and missing nodes
GOstats
updated 14 months ago by
steffi
• 0 • written 14 months ago by
Matthew Thornton
▴ 350
2
votes
3
replies
1.7k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats
GO
RNASeq
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
joasmile84
▴ 20
1
vote
2
replies
903
views
Getting list of genes enriched in each of Biological process terms
GOstats
Go.db
GeneOntology
3.1 years ago
MOHAMMAD
• 0
0
votes
0
replies
759
views
Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE
hypeR
goTools
GOstats
topGO
3.4 years ago
Madza Farias-Virgens
• 0
0
votes
1
reply
807
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats
GO
R
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
ramonmassoni
▴ 10
3
votes
4
replies
1.4k
views
Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3
Cytoscape
Rgraphviz
GOstats
5.0 years ago
Matthew Thornton
▴ 350
0
votes
5
replies
1.5k
views
hyperGTest not working on custom annotation package
GOstats
AnnotationDbi
GO.db
updated 5.2 years ago by
James W. MacDonald
65k • written 5.2 years ago by
lucas.michel
• 0
2
votes
2
replies
1.4k
views
GO.db source obo file?
gene ontology
gostats
go.db
ontologies
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
brismiller
• 0
0
votes
2
replies
1.1k
views
comparing two GOstats result lists
gostats
statistics
updated 5.9 years ago by
James W. MacDonald
65k • written 5.9 years ago by
sven.schenk
▴ 20
3
votes
10
replies
1.3k
views
GO Stats results contain GO terms NOT present in the gene universe
gostats
updated 6.0 years ago by
emmascottgm
• 0 • written 6.0 years ago by
sven.schenk
▴ 20
0
votes
1
reply
1.8k
views
how to run GO enrichment analysis for non-model organisms (errors when using hyperGTest)
gostats
GO
non_model
6.1 years ago
zhaoran1124
• 0
0
votes
0
replies
1.2k
views
GOstats install Error : .onLoad failed in loadNamespace() for 'GO.db'
gostats
go.db
6.2 years ago
crafy
• 0
0
votes
0
replies
1.1k
views
invalid names for slots of class GOHyperGResult
gostats
6.5 years ago
laianavarromartin
▴ 20
0
votes
6
replies
1.6k
views
GO-terms delivered by GOstats hyperGTest() do not exist in my universe
GOstats
6.5 years ago
martis.mihaela
• 0
0
votes
1
reply
1.2k
views
Add gene information to most expressed gene list (packages lumi and GOstats)
annotation
lumi
GOstats
updated 6.6 years ago by
James W. MacDonald
65k • written 6.6 years ago by
marongiu.luigi
• 0
0
votes
0
replies
980
views
Question: Enrichment heatmap - GOstats package of R
Gostats
p-value
6.8 years ago
salamandra
▴ 20
0
votes
1
reply
934
views
GOstats R Package
gostats
6.8 years ago
arpa530
• 0
0
votes
0
replies
1.2k
views
Pathway analysis for diffrential express gene
pathways
gage
annotation
gostats
7.2 years ago
avinash gupta
▴ 130
4
votes
2
replies
1.5k
views
Why do I get different GO term sizes using the same gene universe for 2 analyses with GOstats?
gostats
hypergeometric test
updated 7.2 years ago by
James W. MacDonald
65k • written 7.2 years ago by
tlaguna
▴ 10
6
votes
6
replies
3.4k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound)
Gostats
go term
annotation
drosophila melanogaster
error
updated 7.2 years ago by
tlaguna
▴ 10 • written 7.9 years ago by
nooshin
▴ 300
2
votes
9
replies
4.0k
views
Unable to calculate in parallel what can be calculated on a for loop
biocparallel
foreach
org.hs.eg.db
gostats
updated 7.4 years ago by
Martin Morgan
25k • written 7.5 years ago by
Lluís Revilla Sancho
▴ 730
1
vote
2
replies
1.4k
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology
GO
overrepresentation analysis
missmethyl
gostats
updated 7.7 years ago by
James W. MacDonald
65k • written 7.7 years ago by
graggsd
• 0
2
votes
1
reply
1.2k
views
Is possible to use an organism annotation package in simLL function?
gostats
updated 7.8 years ago by
James W. MacDonald
65k • written 7.8 years ago by
Lluís Revilla Sancho
▴ 730
0
votes
4
replies
1.4k
views
Error in GOFrame due to NA for unsupported organism (Gene Ontology)
reportingtools
annotationhub
gostats
updated 7.8 years ago by
James W. MacDonald
65k • written 7.8 years ago by
cagenet34
▴ 20
0
votes
1
reply
3.6k
views
GOstats - Error in order(pvals) : argument 1 is not a vector
bioconductor
r
gostats
updated 7.9 years ago by
James W. MacDonald
65k • written 7.9 years ago by
sarajdcardoso
• 0
0
votes
2
replies
1.2k
views
broken link to www.godatabase.org in results generated by htmlReport() from GOstats package ?
GOstats
www.godatabase.org
htmlReport
7.9 years ago
c.kohler
• 0
0
votes
3
replies
1.9k
views
Can not install 'affyio' with compiler icc on redhat linux ES5
GOstats
GOstats
updated 7.9 years ago by
dave
▴ 10 • written 13.5 years ago by
Zhenguo Zhang
▴ 10
0
votes
1
reply
1.2k
views
Problem with GOstats - invalid names for slots of class GOHyperGResult
GOstat
GOstats
7.9 years ago
ccanchaya
• 0
0
votes
2
replies
2.9k
views
Odd Odds Ratio in GOstats package
GO
GOstats
GO
GOstats
updated 8.1 years ago by
bannistersc
• 0 • written 10.0 years ago by
Moreno Colaiacovo
▴ 10
0
votes
0
replies
1.3k
views
Annotation, Over representation testing and Pathway analysis using Ensembl gene IDs
rnaseq
annotation
gostats
org.Bt.eg.db
8.1 years ago
mrodrigues.fernanda
▴ 10
13
votes
2
replies
4.6k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA
goseq
topgo
gega
gostats
updated 8.5 years ago by
Robert Castelo
★ 3.3k • written 8.5 years ago by
jacorvar
▴ 40
1
vote
0
replies
1.4k
views
enrichment analysis for gene pairs
go
gostats
category
gsea
8.5 years ago
Hector Corrada Bravo
▴ 60
1
vote
1
reply
1.4k
views
GoStats Hit Counter for website
gostats
gostat
updated 8.6 years ago by
Dan Tenenbaum
★ 8.2k • written 8.6 years ago by
jacob
• 0
0
votes
1
reply
1.4k
views
GOstats and termGraph - Getting all of the plots out of the list
gostats
rgraphviz
updated 8.7 years ago by
Valerie Obenchain
★ 6.8k • written 8.7 years ago by
Matt Thornton
• 0
0
votes
0
replies
1.3k
views
hyperGTest for MSigDB categories
category
gostats
msigdb
hypergeometric test
8.8 years ago
petyuk
▴ 70
0
votes
2
replies
1.2k
views
Conditional test for goseq?
goseq
gostats
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
Johannes Rainer
★ 2.0k
0
votes
8
replies
2.1k
views
PFAM Enrichment in GOstats
PFAM
Category
GOstats
updated 9.0 years ago by
Guangchuang Yu
★ 1.2k • written 9.0 years ago by
Iain Gallagher
▴ 930
1
vote
2
replies
1.3k
views
Mysterious warning message: "...in .local... ignoring 'pos' argument
warnings
gostats
updated 9.0 years ago by
James W. MacDonald
65k • written 9.0 years ago by
jon.young
• 0
0
votes
1
reply
974
views
Alien GO result from GOstats
gostats
9.1 years ago
Yue Zhao
• 0
0
votes
3
replies
1.5k
views
Genes corresponding to GO terms for unsupported organsims
gostats
unsupported organisms
updated 9.2 years ago by
Marc Carlson
★ 7.2k • written 9.2 years ago by
Krys Kelly
▴ 270
1
vote
10
replies
2.3k
views
Filtering genes for GOstats
gostats
9.2 years ago
nonCodingGene
▴ 10
0
votes
1
reply
1.7k
views
Customized GO enrichment with GOstat
GOstats
updated 9.2 years ago by
James W. MacDonald
65k • written 9.2 years ago by
doodlehzq
• 0
0
votes
6
replies
2.2k
views
hyperGTest interpretation of 'under' and finding all Entrez associated with a GO term
Annotation
GO
gostats
updated 9.4 years ago by
Gordon Smyth
50k • written 11.5 years ago by
Mary Kindall
▴ 70
0
votes
2
replies
1.8k
views
Incomplete gene IDs in KEGG pathway testing
gostats
kegg
updated 9.5 years ago by
James W. MacDonald
65k • written 9.5 years ago by
willmacnair
• 0
3
votes
3
replies
2.3k
views
GOstats "count" question
gostats
updated 9.5 years ago by
James W. MacDonald
65k • written 9.5 years ago by
ylc35
▴ 10
4
votes
3
replies
2.8k
views
Select the annotation level during GO enrichment
topgo
gostats
go
updated 9.6 years ago by
James W. MacDonald
65k • written 9.6 years ago by
artur
▴ 80
0
votes
0
replies
2.3k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways
GO
Organism
GOstats
9.7 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.7k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways
GO
Organism
GOstats
9.7 years ago
Guest User
★ 13k
50 results • Page
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Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
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