Package: phruta 0.1.3

Cristian Roman Palacios

phruta: Phylogenetic Reconstruction and Time-dating

The phruta R package is designed to simplify the basic phylogenetic pipeline. Specifically, all code is run within the same program and data from intermediate steps are saved in independent folders. Furthermore, all code is run within the same environment which increases the reproducibility of your analysis. phruta retrieves gene sequences, combines newly downloaded and local gene sequences, and performs sequence alignments.

Authors:Cristian Roman Palacios [aut, cre], Anna Krystalli [rev], Rayna Harris [rev], Frederick Boehm [rev]

phruta_0.1.3.tar.gz
phruta_0.1.3.zip(r-4.5)phruta_0.1.3.zip(r-4.4)phruta_0.1.3.zip(r-4.3)
phruta_0.1.3.tgz(r-4.4-any)phruta_0.1.3.tgz(r-4.3-any)
phruta_0.1.3.tar.gz(r-4.5-noble)phruta_0.1.3.tar.gz(r-4.4-noble)
phruta_0.1.3.tgz(r-4.4-emscripten)phruta_0.1.3.tgz(r-4.3-emscripten)
phruta.pdf |phruta.html✨
phruta/json (API)
NEWS

# Install 'phruta' in R:
install.packages('phruta', repos = c('https://packages.ropensci.org', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ropensci/phruta/issues

Datasets:

    On CRAN:

    13 exports 9 stars 4.75 score 193 dependencies 14 scripts

    Last updated 3 months agofrom:a664f5f2d9 (on main). Checks:OK: 3 ERROR: 3 NOTE: 1. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKSep 28 2024
    R-4.5-winERRORSep 28 2024
    R-4.5-linuxERRORSep 28 2024
    R-4.4-winERRORSep 28 2024
    R-4.4-macNOTESep 28 2024
    R-4.3-winOKSep 28 2024
    R-4.3-macOKSep 28 2024

    Exports:acc.table.retrievegene.sampling.retrievegetListConstraintssq.addsq.alnsq.curatesq.partitionfinderv1sq.retrieve.directsq.retrieve.indirecttree.constrainttree.datingtree.raxmltree.roguetaxa

    Dependencies:apclusterapeaskpassassertthatbackportsbase64encBiocGenericsBiostringsbitbit64bitopsboldbslibcachemcheckmateclassclicliprclusterclusterGenerationcodacodetoolscolorspacecombinatcommonmarkcpp11crayoncrulcurldata.tableDBIDECIPHERDEoptimdeSolvedigestdoParalleldoSNOWdplyre1071evaluateexpmfansifarverfastmapfastmatchfontawesomeforeachforeignFormulafsgeigergenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttpuvhttrigraphipsIRangesisobanditeratorsjquerylibjsonlitekebabskernlabknitrlabelinglaterlatticelazyevalLiblineaRlifecyclemagrittrmapsMASSMatrixmatrixStatsmclustmemoisemgcvmimemnormtmsamunsellmvtnormnatservncbitnlmennetnumDerivoaiodseqopenssloptimParallelpbapplyphangornphytoolspillarpkgconfigPlotToolsplyrprettyunitsprogresspromisesproxypurrrquadprogR.cacheR.methodsS3R.ooR.utilsR6rappdirsratelimitrrbibutilsRColorBrewerRcppRcppArmadilloRcppGSLRcppParallelRcppZigguratRCurlRdpackreadrrentrezreutilsrexRfastrgbifritisrlangrmarkdownrnclRoguerotlrpartrredlistrstudioapiS4Vectorssassscalesscatterplot3dshinyshinyjssnowsolriumsourcetoolsstringistringrsubplexsystaxizetibbletidyselecttinytexTreeDistTreeToolstriebeardtzdbUCSC.utilsurltoolsutf8vctrsviridisviridisLitevroomwhiskerWikidataQueryServiceRWikidataRWikipediRwikitaxawithrwkworrmsxfunXMLxml2xtableXVectoryamlzlibbioczoo

    Advanced methods

    Rendered fromPhruta_advanced.Rmdusingknitr::rmarkdownon Sep 28 2024.

    Last update: 2023-01-06
    Started: 2021-08-24

    Future directions for phruta

    Cristian Román-Palacios

    Rendered fromFuture_phruta.Rmdusingknitr::rmarkdownon Sep 28 2024.

    Last update: 2023-01-06
    Started: 2022-05-30

    Getting started with phruta

    Rendered fromphruta.Rmdusingknitr::rmarkdownon Sep 28 2024.

    Last update: 2023-01-06
    Started: 2022-06-29

    phruta behind the scenes

    Cristian Román-Palacios

    Rendered frompackage_acknowledgements.Rmdusingknitr::rmarkdownon Sep 28 2024.

    Last update: 2023-05-02
    Started: 2023-05-02

    Phylogenetics with phruta

    Rendered fromPhylogenetics_phruta.Rmdusingknitr::rmarkdownon Sep 28 2024.

    Last update: 2023-01-06
    Started: 2022-05-30

    To export or not export phruta outputs

    Rendered fromExporting_data_phruta.Rmdusingknitr::rmarkdownon Sep 28 2024.

    Last update: 2023-01-06
    Started: 2022-06-02

    Usando el paquete de R phruta

    Rendered fromusando_phruta.Rmdusingknitr::rmarkdownon Sep 28 2024.

    Last update: 2023-01-06
    Started: 2022-06-29

    Using phruta with a defined set of target genes

    Rendered fromphruta_targetgenes.Rmdusingknitr::rmarkdownon Sep 28 2024.

    Last update: 2023-01-06
    Started: 2022-06-28

    Using the phruta R package

    Rendered fromUsing_phruta.Rmdusingknitr::rmarkdownon Sep 28 2024.

    Last update: 2023-01-06
    Started: 2022-06-02