Showing : GOstats • reset
0
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Gene Ontology (GO) Analysis
GOstats hyperGTest GO enrichGO clusterProfiler
29 days ago • updated 8 days ago GA ▴ 10
0
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2
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859
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GOstats kegg analysis in wheat - help - none of the objects in the first column are legitimate kegg ids (but they are)
AnnotationDbi GOstats
6 months ago GV Yoshikawa • 0
0
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0
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640
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Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
22 months ago georgii.vdovin • 0
0
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0
replies
687
views
plotGOTermGraph connects all subtrees to the root node
GO.db GOstats
23 months ago RuBBiT0 ▴ 10
1
vote
9
replies
1.8k
views
GOstats - subsetting termGraphs with terms from the html report and missing nodes
GOstats
updated 2.2 years ago by • 0 • written 2.2 years ago by ▴ 380
2
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3
replies
2.4k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 20
1
vote
2
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1.2k
views
Getting list of genes enriched in each of Biological process terms
GOstats Go.db GeneOntology
4.2 years ago MOHAMMAD • 0
0
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0
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1.0k
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Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
4.5 years ago Madza Farias-Virgens • 0
0
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1
reply
1.1k
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 10
3
votes
4
replies
1.8k
views
Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3 Cytoscape Rgraphviz GOstats
6.0 years ago Matthew Thornton ▴ 380
0
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5
replies
1.9k
views
hyperGTest not working on custom annotation package
GOstats AnnotationDbi GO.db
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
2
votes
2
replies
1.7k
views
GO.db source obo file?
gene ontology gostats go.db ontologies
updated 6.8 years ago by 25k • written 6.8 years ago by • 0
0
votes
2
replies
1.4k
views
comparing two GOstats result lists
gostats statistics
updated 7.0 years ago by 68k • written 7.0 years ago by ▴ 30
3
votes
10
replies
1.8k
views
GO Stats results contain GO terms NOT present in the gene universe
gostats
updated 7.0 years ago by • 0 • written 7.0 years ago by ▴ 30
0
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1
reply
2.1k
views
how to run GO enrichment analysis for non-model organisms (errors when using hyperGTest)
gostats GO non_model
7.1 years ago zhaoran1124 • 0
0
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0
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1.5k
views
GOstats install Error : .onLoad failed in loadNamespace() for 'GO.db'
gostats go.db
7.2 years ago crafy • 0
0
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0
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1.5k
views
invalid names for slots of class GOHyperGResult
gostats
7.5 years ago laianavarromartin ▴ 20
0
votes
6
replies
2.1k
views
GO-terms delivered by GOstats hyperGTest() do not exist in my universe
GOstats
7.5 years ago martis.mihaela • 0
0
votes
1
reply
1.5k
views
Add gene information to most expressed gene list (packages lumi and GOstats)
annotation lumi GOstats
updated 7.6 years ago by 68k • written 7.6 years ago by • 0
0
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0
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1.2k
views
Question: Enrichment heatmap - GOstats package of R
Gostats p-value
7.8 years ago salamandra ▴ 20
0
votes
1
reply
1.1k
views
GOstats R Package
gostats
7.9 years ago arpa530 • 0
0
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0
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1.5k
views
Pathway analysis for diffrential express gene
pathways gage annotation gostats
8.2 years ago avinash gupta ▴ 130
4
votes
2
replies
1.8k
views
Why do I get different GO term sizes using the same gene universe for 2 analyses with GOstats?
gostats hypergeometric test
updated 8.3 years ago by 68k • written 8.3 years ago by ▴ 10
6
votes
6
replies
4.0k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound)
Gostats go term annotation drosophila melanogaster error
updated 8.3 years ago by ▴ 10 • written 9.0 years ago by ▴ 300
2
votes
9
replies
4.5k
views
Unable to calculate in parallel what can be calculated on a for loop
biocparallel foreach org.hs.eg.db gostats
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 760
1
vote
2
replies
1.8k
views
Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology GO overrepresentation analysis missmethyl gostats
updated 8.8 years ago by 68k • written 8.8 years ago by • 0
2
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1
reply
1.4k
views
Is possible to use an organism annotation package in simLL function?
gostats
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 760
0
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4
replies
1.8k
views
Error in GOFrame due to NA for unsupported organism (Gene Ontology)
reportingtools annotationhub gostats
updated 8.9 years ago by 68k • written 8.9 years ago by ▴ 20
0
votes
1
reply
4.0k
views
GOstats - Error in order(pvals) : argument 1 is not a vector
bioconductor r gostats
updated 8.9 years ago by 68k • written 8.9 years ago by • 0
0
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2
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1.5k
views
broken link to www.godatabase.org in results generated by htmlReport() from GOstats package ?
GOstats www.godatabase.org htmlReport
8.9 years ago c.kohler • 0
0
votes
3
replies
2.2k
views
Can not install 'affyio' with compiler icc on redhat linux ES5
GOstats GOstats
updated 8.9 years ago by ▴ 10 • written 14.5 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
8.9 years ago ccanchaya • 0
0
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2
replies
3.3k
views
Odd Odds Ratio in GOstats package
GO GOstats GO GOstats
updated 9.1 years ago by • 0 • written 11.1 years ago by ▴ 10
0
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0
replies
1.6k
views
Annotation, Over representation testing and Pathway analysis using Ensembl gene IDs
rnaseq annotation gostats org.Bt.eg.db
9.1 years ago mrodrigues.fernanda ▴ 10
13
votes
2
replies
5.2k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA goseq topgo gega gostats
updated 9.5 years ago by ★ 3.4k • written 9.5 years ago by ▴ 40
1
vote
0
replies
1.6k
views
enrichment analysis for gene pairs
go gostats category gsea
9.6 years ago Hector Corrada Bravo ▴ 60
1
vote
1
reply
1.6k
views
GoStats Hit Counter for website
gostats gostat
updated 9.6 years ago by ★ 8.2k • written 9.6 years ago by • 0
0
votes
1
reply
1.6k
views
GOstats and termGraph - Getting all of the plots out of the list
gostats rgraphviz
updated 9.8 years ago by ★ 6.8k • written 9.8 years ago by • 0
0
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0
replies
1.6k
views
hyperGTest for MSigDB categories
category gostats msigdb hypergeometric test
9.8 years ago petyuk ▴ 70
0
votes
2
replies
1.4k
views
Conditional test for goseq?
goseq gostats
updated 9.8 years ago by 52k • written 9.8 years ago by ★ 2.1k
0
votes
8
replies
2.5k
views
PFAM Enrichment in GOstats
PFAM Category GOstats
updated 10.0 years ago by ★ 1.2k • written 10.0 years ago by ▴ 930
1
vote
2
replies
1.6k
views
Mysterious warning message: "...in .local... ignoring 'pos' argument
warnings gostats
updated 10.1 years ago by 68k • written 10.1 years ago by • 0
0
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1
reply
1.2k
views
Alien GO result from GOstats
gostats
10.1 years ago Yue Zhao • 0
0
votes
3
replies
1.9k
views
Genes corresponding to GO terms for unsupported organsims
gostats unsupported organisms
updated 10.2 years ago by ★ 7.2k • written 10.2 years ago by ▴ 270
1
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10
replies
2.8k
views
Filtering genes for GOstats
gostats
10.3 years ago nonCodingGene ▴ 10
0
votes
1
reply
1.9k
views
Customized GO enrichment with GOstat
GOstats
updated 10.3 years ago by 68k • written 10.3 years ago by • 0
0
votes
6
replies
2.6k
views
hyperGTest interpretation of 'under' and finding all Entrez associated with a GO term
Annotation GO gostats
updated 10.4 years ago by 52k • written 12.5 years ago by ▴ 70
0
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2
replies
2.2k
views
Incomplete gene IDs in KEGG pathway testing
gostats kegg
updated 10.5 years ago by 68k • written 10.5 years ago by • 0
3
votes
3
replies
2.8k
views
GOstats "count" question
gostats
updated 10.6 years ago by 68k • written 10.6 years ago by ▴ 10
4
votes
3
replies
3.7k
views
Select the annotation level during GO enrichment
topgo gostats go
updated 10.6 years ago by 68k • written 10.6 years ago by ▴ 80
50 results • Page 1 of 1
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Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr by Paul Harrison ▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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Popular Question to Gordon Smyth 52k
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