rPlant: Interface to the Agave API

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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.

Author
Barb 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 publication
2016-04-03 16:38:09
Maintainer
Kurt Michels <kamichels@math.arizona.edu>
License
GPL (>= 2)
Version
2.16
URLs

View on CRAN

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

Files in this package

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