rPlant: Interface to the Agave API

Provides an interface to the the many computational resources iPlant offers through their RESTful application programming interface, see <http://www.iplantcollaborative.org/> for more information about iPlant, and <http://www.iplantcollaborative.org/ci/iplant-science-apis> 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 <http://agaveapi.co/> for more information on the Agave API and <http://user.iplantcollaborative.org/> to register with iPlant.

Install the latest version of this package by entering the following in R:
install.packages("rPlant")
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
http://www.iplantcollaborative.org/discover/discovery-environment

View on CRAN

Functions

appINFO Man page
Check Man page
CheckJobStatus Man page
clustal Man page
Clustal Man page
ClustalW Man page
CompareNames Man page
CopyDir Man page
CopyFile Man page
DeleteDir Man page
DeleteFile Man page
DeleteJob Man page
DNA.fasta Man page
Error Man page
fasta_aa.aln Man page
fasta_dna.aln Man page
FaST_LMM Man page
fasttree Man page
Fasttree Man page
FastTree Man page
find.input Man page
geno_test.tfam Man page
geno_test.tped 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
PermissionsDir Man page
PermissionsFile Man page
phylip_interleaved_aa.aln Man page
phylip_interleaved_dna.aln Man page
PLINK Man page
PLINKConversion Man page
PROTEIN.fasta Man page
raxml 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
rplant Man page
rPlant Man page
rplant.env Man page
rplant-package Man page
ShareDir Man page
ShareFile Man page
simulation1.map Man page
simulation1.ped Man page
SubmitJob Man page
SupportFile Man page
TestApp Man page
Time Man page
TNRS Man page
UploadFile Man page
Validate Man page
Wait 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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.