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

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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.

Author
I. Richard Thompson [aut, cre]
Date of publication
2016-09-21 12:35:11
Maintainer
I. Richard Thompson <ithompson@qf.org.qa>
License
GPL-3
Version
0.1.6

View on CRAN

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...

Files in this package

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