Showing : gostats • reset
0
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3
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1.2k
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Gene Ontology (GO) Analysis
GOstats hyperGTest GO enrichGO clusterProfiler
6 months ago • updated 5 months ago GA ▴ 10
0
votes
2
replies
958
views
GOstats kegg analysis in wheat - help - none of the objects in the first column are legitimate kegg ids (but they are)
AnnotationDbi GOstats
11 months ago GV Yoshikawa • 0
0
votes
0
replies
781
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
2.3 years ago georgii.vdovin • 0
0
votes
0
replies
786
views
plotGOTermGraph connects all subtrees to the root node
GO.db GOstats
2.4 years ago RuBBiT0 ▴ 10
1
vote
9
replies
2.0k
views
GOstats - subsetting termGraphs with terms from the html report and missing nodes
GOstats
updated 2.6 years ago by • 0 • written 2.6 years ago by ▴ 380
2
votes
3
replies
2.6k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 3.9 years ago by 68k • written 3.9 years ago by ▴ 20
1
vote
2
replies
1.3k
views
Getting list of genes enriched in each of Biological process terms
GOstats Go.db GeneOntology
4.6 years ago MOHAMMAD • 0
0
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0
replies
1.1k
views
Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
4.9 years ago Madza Farias-Virgens • 0
0
votes
1
reply
1.2k
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 10
3
votes
4
replies
2.0k
views
Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3 Cytoscape Rgraphviz GOstats
6.5 years ago • updated 6.4 years ago Matthew Thornton ▴ 380
0
votes
5
replies
2.0k
views
hyperGTest not working on custom annotation package
GOstats AnnotationDbi GO.db
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
2
votes
2
replies
1.9k
views
GO.db source obo file?
gene ontology gostats go.db ontologies
updated 7.2 years ago by 25k • written 7.2 years ago by • 0
0
votes
2
replies
1.5k
views
comparing two GOstats result lists
gostats statistics
updated 7.4 years ago by 68k • written 7.4 years ago by ▴ 30
3
votes
10
replies
1.9k
views
GO Stats results contain GO terms NOT present in the gene universe
gostats
updated 7.4 years ago by • 0 • written 7.4 years ago by ▴ 30
0
votes
1
reply
2.3k
views
how to run GO enrichment analysis for non-model organisms (errors when using hyperGTest)
gostats GO non_model
7.5 years ago zhaoran1124 • 0
0
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0
replies
1.5k
views
GOstats install Error : .onLoad failed in loadNamespace() for 'GO.db'
gostats go.db
7.6 years ago crafy • 0
0
votes
0
replies
1.6k
views
invalid names for slots of class GOHyperGResult
gostats
7.9 years ago laianavarromartin ▴ 20
0
votes
6
replies
2.2k
views
GO-terms delivered by GOstats hyperGTest() do not exist in my universe
GOstats
8.0 years ago martis.mihaela • 0
0
votes
1
reply
1.6k
views
Add gene information to most expressed gene list (packages lumi and GOstats)
annotation lumi GOstats
updated 8.1 years ago by 68k • written 8.1 years ago by • 0
0
votes
0
replies
1.3k
views
Question: Enrichment heatmap - GOstats package of R
Gostats p-value
8.3 years ago salamandra ▴ 20
0
votes
1
reply
1.2k
views
GOstats R Package
gostats
8.3 years ago arpa530 • 0
0
votes
0
replies
1.6k
views
Pathway analysis for diffrential express gene
pathways gage annotation gostats
8.7 years ago avinash gupta ▴ 130
4
votes
2
replies
1.9k
views
Why do I get different GO term sizes using the same gene universe for 2 analyses with GOstats?
gostats hypergeometric test
updated 8.7 years ago by 68k • written 8.7 years ago by ▴ 10
6
votes
6
replies
4.2k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound)
Gostats go term annotation drosophila melanogaster error
updated 8.7 years ago by ▴ 10 • written 9.4 years ago by ▴ 300
2
votes
9
replies
4.8k
views
Unable to calculate in parallel what can be calculated on a for loop
biocparallel foreach org.hs.eg.db gostats
updated 8.9 years ago by 25k • written 9.0 years ago by ▴ 760
1
vote
2
replies
2.0k
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology GO overrepresentation analysis missmethyl gostats
updated 9.2 years ago by 68k • written 9.2 years ago by • 0
2
votes
1
reply
1.5k
views
Is possible to use an organism annotation package in simLL function?
gostats
updated 9.2 years ago by 68k • written 9.2 years ago by ▴ 760
0
votes
4
replies
1.9k
views
Error in GOFrame due to NA for unsupported organism (Gene Ontology)
reportingtools annotationhub gostats
updated 9.3 years ago by 68k • written 9.3 years ago by ▴ 20
0
votes
1
reply
4.1k
views
GOstats - Error in order(pvals) : argument 1 is not a vector
bioconductor r gostats
updated 9.3 years ago by 68k • written 9.3 years ago by • 0
0
votes
2
replies
1.6k
views
broken link to www.godatabase.org in results generated by htmlReport() from GOstats package ?
GOstats www.godatabase.org htmlReport
9.3 years ago c.kohler • 0
0
votes
3
replies
2.4k
views
Can not install 'affyio' with compiler icc on redhat linux ES5
GOstats GOstats
updated 9.3 years ago by ▴ 10 • written 14.9 years ago by ▴ 10
0
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1
reply
1.5k
views
Problem with GOstats - invalid names for slots of class GOHyperGResult
GOstat GOstats
9.4 years ago ccanchaya • 0
0
votes
2
replies
3.4k
views
Odd Odds Ratio in GOstats package
GO GOstats GO GOstats
updated 9.6 years ago by • 0 • written 11.5 years ago by ▴ 10
0
votes
0
replies
1.7k
views
Annotation, Over representation testing and Pathway analysis using Ensembl gene IDs
rnaseq annotation gostats org.Bt.eg.db
9.6 years ago mrodrigues.fernanda ▴ 10
13
votes
2
replies
5.4k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA goseq topgo gega gostats
updated 9.9 years ago by ★ 3.4k • written 9.9 years ago by ▴ 40
1
vote
0
replies
1.7k
views
enrichment analysis for gene pairs
go gostats category gsea
10.0 years ago Hector Corrada Bravo ▴ 60
1
vote
1
reply
1.7k
views
GoStats Hit Counter for website
gostats gostat
updated 10.1 years ago by ★ 8.2k • written 10.1 years ago by • 0
0
votes
1
reply
1.7k
views
GOstats and termGraph - Getting all of the plots out of the list
gostats rgraphviz
updated 10.2 years ago by ★ 6.8k • written 10.2 years ago by • 0
0
votes
0
replies
1.6k
views
hyperGTest for MSigDB categories
category gostats msigdb hypergeometric test
10.2 years ago petyuk ▴ 70
0
votes
2
replies
1.5k
views
Conditional test for goseq?
goseq gostats
updated 10.2 years ago by 53k • written 10.3 years ago by ★ 2.1k
0
votes
8
replies
2.7k
views
PFAM Enrichment in GOstats
PFAM Category GOstats
updated 10.5 years ago by ★ 1.2k • written 10.5 years ago by ▴ 930
1
vote
2
replies
1.7k
views
Mysterious warning message: "...in .local... ignoring 'pos' argument
warnings gostats
updated 10.5 years ago by 68k • written 10.5 years ago by • 0
0
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1
reply
1.2k
views
Alien GO result from GOstats
gostats
10.5 years ago Yue Zhao • 0
0
votes
3
replies
2.1k
views
Genes corresponding to GO terms for unsupported organsims
gostats unsupported organisms
updated 10.6 years ago by ★ 7.2k • written 10.6 years ago by ▴ 270
1
vote
10
replies
3.0k
views
Filtering genes for GOstats
gostats
10.7 years ago nonCodingGene ▴ 10
0
votes
1
reply
2.0k
views
Customized GO enrichment with GOstat
GOstats
updated 10.7 years ago by 68k • written 10.7 years ago by • 0
0
votes
6
replies
2.7k
views
hyperGTest interpretation of 'under' and finding all Entrez associated with a GO term
Annotation GO gostats
updated 10.9 years ago by 53k • written 13.0 years ago by ▴ 70
0
votes
2
replies
2.3k
views
Incomplete gene IDs in KEGG pathway testing
gostats kegg
updated 10.9 years ago by 68k • written 11.0 years ago by • 0
3
votes
3
replies
3.0k
views
GOstats "count" question
gostats
updated 11.0 years ago by 68k • written 11.0 years ago by ▴ 10
4
votes
3
replies
3.8k
views
Select the annotation level during GO enrichment
topgo gostats go
updated 11.1 years ago by 68k • written 11.1 years ago by ▴ 80
250 results • Page 1 of 5
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Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
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A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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