ungeneanno: Collate Gene Annotation Data from Uniprot and NIH Gene Databases
Version 0.1.6

Taking a list of genes, the package collates together the summary information about those genes from the publicly available resources at Uniprot and NCBI. Additionally, the package is able to collate publication information from a search of the NCBI Pubmed database.

Browse man pages Browse package API and functions Browse package files

AuthorI. Richard Thompson [aut, cre]
Date of publication2016-09-21 12:35:11
MaintainerI. Richard Thompson <ithompson@qf.org.qa>
LicenseGPL-3
Version0.1.6
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ungeneanno")

Man pages

geneanno-class: An S4 class to represent the base information used by the...
gene-class: An S4 class to represent a gene.
genematrix: Input Matrix of Drug/Gene Data
getGeneSummary: Create gene specific objects containing data from online...
getGroupGeneList: Create unique list of group,gene combinations from input list
getNihQuery: create initial NIH Query
getNihSummary: Gather NIH Gene Data
getPublicationList: Gather NIH Pubmed Data
getUniprotSummary: Gather Uniprot Data
getUniqueGeneList: Create unique list of genes from input list
inputlist: Input Vector of Drug/Gene Data
parseInputFile: Parse files of gene names and group identifiers to create...
produceOutputFiles: Save Gene Information to group Specific Output Files
pubmed-class: An S4 class to represent a query to the Pubmed database,...
query-class: An S4 class to represent an initial query to the NCBI...
searchPublications: Carry out Pubmed search for a mtrix
ungeneanno-package: Collate Gene Annotation Data from Uniprot and NIH Gene...

Functions

gene Man page
gene-class Man page
geneanno Man page
geneanno-class Man page
genematrix Man page
getGeneSummary Man page
getGeneSummary,geneanno-method Man page
getGroupGeneList Man page
getGroupGeneList,geneanno,character-method Man page
getGroupGeneList,geneanno,matrix-method Man page
getNihQuery Man page
getNihQuery,query-method Man page
getNihSummary Man page
getNihSummary,gene-method Man page
getPublicationList Man page
getPublicationList,character-method Man page
getUniprotSummary Man page
getUniprotSummary,gene-method Man page
getUniqueGeneList Man page
getUniqueGeneList,geneanno,character-method Man page
getUniqueGeneList,geneanno,matrix-method Man page
inputlist Man page
parseInputFile Man page
parseInputFile,geneanno-method Man page
produceOutputFiles Man page
produceOutputFiles,geneanno,vector,vector,missing-method Man page
produceOutputFiles,geneanno,vector,vector,vector-method Man page
pubmed Man page
pubmed-class Man page
query Man page
query-class Man page
searchPublications Man page
searchPublications,matrix-method Man page
ungeneanno Man page
ungeneanno-package Man page

Files

inst
inst/doc
inst/doc/Complete_examples.Rmd
inst/doc/PubMed_Query_Example.Rmd
inst/doc/Complete_examples.html
inst/doc/Complete_examples.R
inst/doc/PubMed_Query_Example.html
tests
tests/testthat.R
tests/testthat
tests/testthat/test-NIHPubMedConnections.R
tests/testthat/test-NIHConnections.R
tests/testthat/uniprot_test_gene.rds
tests/testthat/ncbi_test_pubmed2.rds
tests/testthat/test-getUniqueGeneList.R
tests/testthat/test-UniportConnections.R
tests/testthat/test-getGroupGeneList.R
tests/testthat/ncbi_test_gene.rds
tests/testthat/ncbi_test_pubmed.rds
NAMESPACE
NEWS
data
data/genematrix.rda
data/inputlist.rda
R
R/GeneAnno.R
R/data.R
R/Pubmed.R
R/NCBI.R
R/ungeneanno.R
R/GeneAnnoClasses.R
R/Uniprot.R
vignettes
vignettes/Complete_examples.Rmd
vignettes/PubMed_Query_Example.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/getNihQuery.Rd
man/gene-class.Rd
man/inputlist.Rd
man/getUniprotSummary.Rd
man/genematrix.Rd
man/produceOutputFiles.Rd
man/pubmed-class.Rd
man/getUniqueGeneList.Rd
man/getGroupGeneList.Rd
man/getPublicationList.Rd
man/ungeneanno-package.Rd
man/geneanno-class.Rd
man/getNihSummary.Rd
man/getGeneSummary.Rd
man/searchPublications.Rd
man/parseInputFile.Rd
man/query-class.Rd
ungeneanno documentation built on May 19, 2017, 11:16 a.m.