rPlant: R interface to the Agave and Foundation API
Version 2.11

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.

Browse man pages Browse package API and functions Browse package files

AuthorBarb 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 publication2015-09-03 03:23:47
MaintainerKurt Michels <kamichels@math.arizona.edu>
LicenseGPL (>= 2)
Version2.11
URL http://www.iplantcollaborative.org/discover/discovery-environment
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rPlant", repos="http://R-Forge.R-project.org")

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

Functions

Check Man page Source code
CheckJobStatus Man page Source code
Clustal Man page
ClustalW Man page Source code
CompareNames Man page Source code
Copy Source code
CopyDir Man page Source code
CopyFile Man page Source code
Create_Keys Source code
DNA.fasta Man page
Delete Source code
DeleteALL Source code
DeleteDir Man page Source code
DeleteFile Man page Source code
DeleteJob Man page Source code
DeleteOne Source code
Error Man page Source code
FaST_LMM Man page Source code
FastTree Man page
Fasttree Man page Source code
GetAppInfo Man page Source code
GetJobHistory Man page Source code
GetPhylotasticToken Man page Source code
KillJob Man page Source code
ListApps Man page Source code
ListDir Man page Source code
ListJobOutput Man page Source code
Mafft Man page Source code
MakeDir Man page Source code
Move Source code
MoveDir Man page Source code
MoveFile Man page Source code
Muscle Man page Source code
PHYLIP_Pars Man page Source code
PLINK Man page Source code
PLINKConversion Man page Source code
PROTEIN.fasta Man page
Pems Source code
PermissionsDir Man page Source code
PermissionsFile Man page Source code
RAXML Man page
RAxML Man page Source code
Raxml Man page
Rename Source code
RenameDir Man page Source code
RenameFile Man page Source code
Renew Man page Source code
RenewToken Man page Source code
ResolveNames Man page Source code
RetrieveJob Man page Source code
RetrieveOne Source code
RetrieveTNRSNames Man page Source code
Share Source code
ShareDir Man page Source code
ShareFile Man page Source code
SubmitJob Man page Source code
SupportFile Man page Source code
TNRS Man page
TestApp Man page Source code
Time Man page Source code
UploadFile Man page Source code
Validate Man page Source code
Wait Man page Source code
appINFO Man page Source code
clustal Man page
fasttree Man page
find.input Man page Source code
geno_test.tfam Man page
geno_test.tped Man page
rPlant Man page
raxml Man page
rplant Man page
rplant-package Man page

Files

DESCRIPTION
NAMESPACE
R
R/ClustalW.R
R/FaST_LMM.R
R/Fasttree.R
R/Mafft.R
R/Muscle.R
R/PHYLIP_Pars.R
R/PLINK.R
R/PLINKConversion.R
R/RAxML.R
R/TNRS.R
R/find.input.R
R/rPlant.R
data
data/DNA.fasta.rda
data/PROTEIN.fasta.rda
data/geno_test.tfam.rda
data/geno_test.tped.rda
inst
inst/doc
inst/doc/TNRSVignette.Rnw
inst/doc/TNRSVignette.pdf
inst/doc/jasa.bst
inst/doc/rPlantVignette.Rnw
inst/doc/rPlantVignette.pdf
inst/doc/rPlantVignette_old.Rnw
inst/doc/refs.bib
inst/extdata
inst/extdata/DNA.fasta
inst/extdata/PROTEIN.fasta
inst/extdata/geno_test.tfam
inst/extdata/geno_test.tped
inst/tests
inst/tests/ex_script.R
inst/tests/rPlantUserManual.pdf
man
man/ClustalW.Rd
man/FaST_LMM.Rd
man/Fasttree.Rd
man/GetAppList.Rd
man/ListDir.Rd
man/Mafft.Rd
man/Muscle.Rd
man/PHYLIP_Pars.Rd
man/PLINK.Rd
man/PLINKConversion.Rd
man/RAxML.Rd
man/SubmitJob.Rd
man/TNRS.Rd
man/UploadFile.Rd
man/Validate.Rd
man/rPlant-data.Rd
man/rPlant-internal.Rd
man/rplant-package.Rd
rPlant documentation built on May 21, 2017, 1:31 a.m.