rPlant: R interface to the Agave and Foundation API

rPlant is an R interface to the the many computational resources iPlant offers through their RESTful application programming interface. Currently, rPlant functions interact with the iPlant foundational API, the Taxonomic Name Resolution Service API, and the Phylotastic Taxosaurus API. Before using rPlant, users will have to register with the iPlant Collaborative.

Author
Barb Banbury <bbanbury@utk.edu>, Kurt Michels <kamichels@math.arizona.edu>, Jeremy M. Beaulieu <jeremy.beaulieu@yale.edu>, Brian O'Meara <bomeara@utk.edu>
Date of publication
2015-09-03 03:23:47
Maintainer
Kurt Michels <kamichels@math.arizona.edu>
License
GPL (>= 2)
Version
2.11
URLs

View on R-Forge

Man pages

ClustalW
ClustalW alignment
FaST_LMM
FaST-LMM-2.07
Fasttree
FastTree Dispatcher
GetAppList
Deployed applications
ListDir
Directory management
Mafft
MAFFT Multiple Sequence Alignment
Muscle
MUSCLE alignment
PHYLIP_Pars
PHYLIP 3.69
PLINK
PLINK-1.07
PLINKConversion
PLINKConversion
RAxML
RAxML
rPlant-data
Data Sets
rPlant-internal
Internal Functions
rplant-package
rplant
SubmitJob
Executing analytical applications
TNRS
Resolving Names via TNRS
UploadFile
File management
Validate
Authentication functions

Files in this package

rPlant/DESCRIPTION
rPlant/NAMESPACE
rPlant/R
rPlant/R/ClustalW.R
rPlant/R/FaST_LMM.R
rPlant/R/Fasttree.R
rPlant/R/Mafft.R
rPlant/R/Muscle.R
rPlant/R/PHYLIP_Pars.R
rPlant/R/PLINK.R
rPlant/R/PLINKConversion.R
rPlant/R/RAxML.R
rPlant/R/TNRS.R
rPlant/R/find.input.R
rPlant/R/rPlant.R
rPlant/data
rPlant/data/DNA.fasta.rda
rPlant/data/PROTEIN.fasta.rda
rPlant/data/geno_test.tfam.rda
rPlant/data/geno_test.tped.rda
rPlant/inst
rPlant/inst/doc
rPlant/inst/doc/TNRSVignette.Rnw
rPlant/inst/doc/TNRSVignette.pdf
rPlant/inst/doc/jasa.bst
rPlant/inst/doc/rPlantVignette.Rnw
rPlant/inst/doc/rPlantVignette.pdf
rPlant/inst/doc/rPlantVignette_old.Rnw
rPlant/inst/doc/refs.bib
rPlant/inst/extdata
rPlant/inst/extdata/DNA.fasta
rPlant/inst/extdata/PROTEIN.fasta
rPlant/inst/extdata/geno_test.tfam
rPlant/inst/extdata/geno_test.tped
rPlant/inst/tests
rPlant/inst/tests/ex_script.R
rPlant/inst/tests/rPlantUserManual.pdf
rPlant/man
rPlant/man/ClustalW.Rd
rPlant/man/FaST_LMM.Rd
rPlant/man/Fasttree.Rd
rPlant/man/GetAppList.Rd
rPlant/man/ListDir.Rd
rPlant/man/Mafft.Rd
rPlant/man/Muscle.Rd
rPlant/man/PHYLIP_Pars.Rd
rPlant/man/PLINK.Rd
rPlant/man/PLINKConversion.Rd
rPlant/man/RAxML.Rd
rPlant/man/SubmitJob.Rd
rPlant/man/TNRS.Rd
rPlant/man/UploadFile.Rd
rPlant/man/Validate.Rd
rPlant/man/rPlant-data.Rd
rPlant/man/rPlant-internal.Rd
rPlant/man/rplant-package.Rd