Last data update: 2014.03.03

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R Release (3.2.3)
CranContrib
BioConductor
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 Results 311 - 320 of 182600 found.
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SubmitJob (Package: rPlant) : Executing analytical applications

Functions for executing and managing analytical applications deployed in the iPlant infrastructure
● Data Source: CranContrib
● Keywords:
● Alias: CheckJobStatus, DeleteJob, GetJobHistory, KillJob, ListJobOutput, RetrieveJob, SubmitJob, Wait
● 0 images

Mafft (Package: rPlant) : MAFFT Multiple Sequence Alignment

WRAPPER DEPRECATED
– one can install mafft on Agave API and use this wrapper as a prototype –
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of about 200 sequences), FFT-NS-2 (fast; for alignment of about 10,000 sequences), etc. See http://mafft.cbrc.jp/alignment/software/. The manual is also available here: http://mafft.cbrc.jp/alignment/software/manual/manual.html
● Data Source: CranContrib
● Keywords:
● Alias: Mafft
● 0 images

rplant-package (Package: rPlant) : rplant

R interface to iPlant's Discovery Enviornment and the Taxonomic Name Resolution Service (TNRS)
● Data Source: CranContrib
● Keywords:
● Alias: rplant, rplant-package
● 0 images

ListApps (Package: rPlant) : Deployed applications

Functions for listing applications deployed in the iPlant software infrastructure and information about them.
● Data Source: CranContrib
● Keywords:
● Alias: GetAppInfo, ListApps
● 0 images

ClustalW (Package: rPlant) : ClustalW alignment

An approach for performing multiple alignments of large numbers of amino acid or nucleotide sequences is described. The method is based on first deriving a phylogenetic tree from a matrix of all pairwise sequence similarity scores, obtained using a fast pairwise alignment algorithm. See details on http://www.clustal.org/clustal2/.
● Data Source: CranContrib
● Keywords:
● Alias: Clustal, ClustalW
● 0 images

FaST_LMM (Package: rPlant) : FaST-LMM-2.07

FaST-LMM (Factored Spectrally Transformed Linear Mixed Models) is a program for performing genome-wide association studies (GWAS) on large data sets. The FaST-LMM iPlant APP is described more fully at https://pods.iplantcollaborative.org/wiki/display/DEapps/FaST-LMM. The program details including downloads and further help pages at http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/.
● Data Source: CranContrib
● Keywords:
● Alias: FaST_LMM
● 0 images

PLINKConversion (Package: rPlant) : PLINKConversion

PLINK is an open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner, check https://pods.iplantcollaborative.org/wiki/display/DEapps/PLINK+Conversion for details. This function converts the standard PLINK file formats (Regular (ped/map), Transposed (tped/tfam), and Binary (bed/bim/fam)) to various other PLINK file formats.
● Data Source: CranContrib
● Keywords:
● Alias: PLINKConversion
● 0 images

PLINK (Package: rPlant) : PLINK-1.07

PLINK is an open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner, check https://pods.iplantcollaborative.org/wiki/display/DEapps/PLINK for details.
● Data Source: CranContrib
● Keywords:
● Alias: PLINK
● 0 images

RAxML (Package: rPlant) : RAxML

RAxML (Randomized Accelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic tress. It originally had been derived from fastDNAml which in turn was derived from Joe Felsentein's dnaml which is part of the PHYLIP package. See http://bioinformatics.oxfordjournals.org/content/suppl/2014/01/18/btu033.DC1/NewManual.pdf for details. The app details can be found here: https://pods.iplantcollaborative.org/wiki/display/DEapps/RAxML-8.2.3_small_and_medium.
● Data Source: CranContrib
● Keywords:
● Alias: RAxML
● 0 images

plot.rPower (Package: rPowerSampleSize) :

For an rPower object which has been produced by montecarlo, this function plots the distribution (estimated by Monte-Carlo) of the number of significant results (i.e, the realized values r).
● Data Source: CranContrib
● Keywords:
● Alias: plot.rPower
● 0 images

Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO