bioc-issue-bot
commented
5 years ago Hi @abrionne
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: ViSEAGO
Version: 0.99.0
Title: Visualisation, Semantic similarity, Enrichment Analysis of Gene Ontology
Authors@R: c(
person("Aurelien","Brionne", role=c("aut","cre"),
email="aurelien.brionne@inra.fr"),
person("Amelie","Juanchich", role="aut",
email="amelie.juanchich@inra.fr"),
person("Christelle","Hennequet-Antier", role="aut",
email="christelle.hennequet-antier@inra.fr"))
Depends: R (>= 3.5)
Imports: data.table,
AnnotationDbi,
AnnotationForge,
biomaRt,
dendextend,
DiagrammeR,
GOSemSim,
DT,
dynamicTreeCut,
ggplot2,
GO.db,
heatmaply,
htmltools,
htmlwidgets,
igraph,
org.Mm.eg.db,
methods,
plotly,
topGO,
Rcpp,
RColorBrewer,
Rgraphviz,
R.utils,
scales,
UpSetR,
webshot,
BiocStyle,
knitr,
rmarkdown,
corrplot,
remotes,
BiocManager
Description: The main objective of ViSEAGO workflow is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed ViSEAGO in R to facilitate functional Gene Ontology (GO) analysis of complex experimental design with multiple comparisons of interest. It allows to study large-scale datasets together and visualize GO profiles to capture biological knowledge. It stands for three major concepts: Visualization, Semantic similarity and Enrichment Analysis of Gene Ontology. It provides access to the last current GO annotations, which are retrieved from one of NCBI EntrezGene, Ensembl or Uniprot databases for available species. ViSEAGO extends classical functional GO analysis to focus on functional coherence by aggregating closely related biological themes while studying multiple datasets at once. It provides both a synthetic and detailed view using interactive functionalities respecting the GO graph structure and ensuring functional coherence supplied by semantic similarity. ViSEAGO has been successfully applied on several datasets from different species with a variety of biological questions. Results can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while maintaining reproducibility.
VignetteBuilder: knitr
License: GPL-3 + file LICENSE
Author: Aurelien Brionne [aut, cre],
Amelie Juanchich[aut],
christelle Hennequet-Antier [aut]
Maintainer: Aurelien Brionne <aurelien.brionne@inra.fr>
Repository: forgemia.inra.fr,
bioconductor.org
URL: https://forgemia.inra.fr/UMR-BOA/ViSEAGO,
https://www.bioconductor.org/packages/release/bioc/html/ViSEAGO.html
BugReports: https://forgemia.inra.fr/UMR-BOA/ViSEAGO/issues
biocViews: Software, Annotation, GO, GeneSetEnrichment, MultipleComparison, Clustering, Visualization
RoxygenNote: 6.1.1
Collate:
'genomic_ressource.R'
'Bioconductor2GO.R'
'Ensembl2GO.R'
'EntrezGene2GO.R'
'EntrezGene_orthologs.R'
'enrich_GO_terms.R'
'GO_SS.R'
'GO_clusters.R'
'GOclusters_heatmap.R'
'GOcount.R'
'GOterms_heatmap.R'
'MDSplot.R'
'Uniprot2GO.R'
'Upset.R'
'annotate.R'
'available_organisms.R'
'build_GO_SS.R'
'clusters_cor.R'
'compare_clusters.R'
'compute_SS_distances.R'
'create_topGOdata.R'
'datasets.R'
'gene2GO.R'
'merge_enrich_terms.R'
'overlapper.R'
'pkgdiagram.R'
'show_heatmap.R'
'show_table.R'
'taxonomy.R'
lshep
ghost
nturaga
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
Confirm the following by editing each check box to '[x]'
[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
I am familiar with the essential aspects of Bioconductor software management, including:
For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.