rPlant: Interface to the Agave API
Version 2.16

Provides an interface to the the many computational resources iPlant offers through their RESTful application programming interface, see for more information about iPlant, and for its APIs. Currently, 'rPlant' functions interact with the iPlant Agave API, the Taxonomic Name Resolution Service API, and the Phylotastic Taxosaurus API. Before using 'rPlant', users will have to register with the iPlant Collaborative. See for more information on the Agave API and to register with iPlant.

Browse man pages Browse package API and functions Browse package files

AuthorBarb Banbury <darwinthesun@gmail.com> and Kurt Michels <kamichels@math.arizona.edu>, Jeremy M. Beaulieu <jeremy.beaulieu@yale.edu>, Brian O'Meara <bomeara@utk.edu>
Date of publication2016-04-03 16:38:09
MaintainerKurt Michels <kamichels@math.arizona.edu>
LicenseGPL (>= 2)
Version2.16
URL http://www.iplantcollaborative.org/discover/discovery-environment
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rPlant")

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
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

Functions

Check Man page
CheckJobStatus Man page
Clustal Man page
ClustalW Man page
CompareNames Man page
CopyDir Man page
CopyFile Man page
DNA.fasta Man page
DeleteDir Man page
DeleteFile Man page
DeleteJob Man page
Error Man page
FaST_LMM Man page
FastTree Man page
Fasttree Man page
GetAppInfo Man page
GetJobHistory Man page
GetPhylotasticToken Man page
KillJob Man page
ListApps Man page
ListDir Man page
ListJobOutput Man page
Mafft Man page
MakeDir Man page
MoveDir Man page
MoveFile Man page
Muscle Man page
PLINK Man page
PLINKConversion Man page
PROTEIN.fasta Man page
PermissionsDir Man page
PermissionsFile Man page
RAXML Man page
RAxML Man page
Raxml Man page
RenameDir Man page
RenameFile Man page
Renew Man page
RenewToken Man page
ResolveNames Man page
RetrieveJob Man page
RetrieveTNRSNames Man page
ShareDir Man page
ShareFile Man page
SubmitJob Man page
SupportFile Man page
TNRS Man page
TestApp Man page
Time Man page
UploadFile Man page
Validate Man page
Wait Man page
appINFO Man page
clustal Man page
fasta_aa.aln Man page
fasta_dna.aln Man page
fasttree Man page
find.input Man page
geno_test.tfam Man page
geno_test.tped Man page
phylip_interleaved_aa.aln Man page
phylip_interleaved_dna.aln Man page
rPlant Man page
raxml Man page
rplant Man page
rplant-package Man page
rplant.env Man page
simulation1.map Man page
simulation1.ped Man page

Files

inst
inst/tests
inst/tests/ex_script.R
inst/tests/rPlantUserManual.pdf
inst/extdata
inst/extdata/geno_test.tped
inst/extdata/geno_test.tfam
inst/extdata/DNA.fasta
inst/extdata/PROTEIN.fasta
NAMESPACE
data
data/simulation1.ped.rda
data/phylip_interleaved_aa.aln.rda
data/simulation1.map.rda
data/PROTEIN.fasta.rda
data/DNA.fasta.rda
data/geno_test.tped.rda
data/fasta_dna.aln.rda
data/geno_test.tfam.rda
data/phylip_interleaved_dna.aln.rda
data/fasta_aa.aln.rda
R
R/PLINKConversion.R
R/rPlant.R
R/Fasttree.R
R/Mafft.R
R/TNRS.R
R/RAxML.R
R/Muscle.R
R/ClustalW.R
R/find.input.R
R/help.R
R/PLINK.R
R/FaST_LMM.R
vignettes
vignettes/rPlantVignette.pdf
vignettes/TNRSVignette.pdf
MD5
DESCRIPTION
man
man/UploadFile.Rd
man/TNRS.Rd
man/ListDir.Rd
man/Fasttree.Rd
man/rPlant-internal.Rd
man/Validate.Rd
man/Muscle.Rd
man/SubmitJob.Rd
man/Mafft.Rd
man/rplant-package.Rd
man/GetAppList.Rd
man/ClustalW.Rd
man/FaST_LMM.Rd
man/PLINKConversion.Rd
man/PLINK.Rd
man/RAxML.Rd
man/rPlant-data.Rd
rPlant documentation built on April 14, 2017, 6:03 p.m.