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:
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')) |
Bug tracker:https://github.com/ropensci/phruta/issues
Last updated 3 months agofrom:a664f5f2d9 (on main). Checks:OK: 3 ERROR: 3 NOTE: 1. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 28 2024 |
R-4.5-win | ERROR | Sep 28 2024 |
R-4.5-linux | ERROR | Sep 28 2024 |
R-4.4-win | ERROR | Sep 28 2024 |
R-4.4-mac | NOTE | Sep 28 2024 |
R-4.3-win | OK | Sep 28 2024 |
R-4.3-mac | OK | Sep 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.Rmd
usingknitr::rmarkdown
on Sep 28 2024.Last update: 2023-01-06
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Future directions for phruta
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usingknitr::rmarkdown
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Getting started with phruta
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phruta behind the scenes
Rendered frompackage_acknowledgements.Rmd
usingknitr::rmarkdown
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Phylogenetics with phruta
Rendered fromPhylogenetics_phruta.Rmd
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on Sep 28 2024.Last update: 2023-01-06
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To export or not export phruta outputs
Rendered fromExporting_data_phruta.Rmd
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on Sep 28 2024.Last update: 2023-01-06
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Usando el paquete de R phruta
Rendered fromusando_phruta.Rmd
usingknitr::rmarkdown
on Sep 28 2024.Last update: 2023-01-06
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Using phruta with a defined set of target genes
Rendered fromphruta_targetgenes.Rmd
usingknitr::rmarkdown
on Sep 28 2024.Last update: 2023-01-06
Started: 2022-06-28
Using the phruta R package
Rendered fromUsing_phruta.Rmd
usingknitr::rmarkdown
on Sep 28 2024.Last update: 2023-01-06
Started: 2022-06-02
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Retrieve accession numbers and titles for a given combination of species and genes in genbank | acc.table.retrieve |
Retrieve the distribution of genes for given organism in genbank | gene.sampling.retrieve |
Add local sequences to previously downloaded sequences | sq.add |
Align sequences | sq.aln |
Curate sequences from genbank | sq.curate |
Run Partitionfinder v.1 | sq.partitionfinderv1 |
Retrieve sequences from genbank | sq.retrieve.direct |
Retrieve sequences from genbank based on a dataset of accession numbers | sq.retrieve.indirect |
Tree inference under RAxML | tree.constraint |
Tree dating under treePL or | tree.dating |
Tree inference under RAxML | tree.raxml |
RogueNaRok within phruta | tree.roguetaxa |