{"Type":"Package","Package":"anndata","Title":"'anndata' for R","Version":"0.7.5.2","Authors@R":"\nc(person(given = \"Philipp\",\nfamily = \"Angerer\",\nrole = \"ccp\",\nemail = \"phil.angerer@gmail.com\",\ncomment = c(ORCID = \"0000-0002-0369-2888\", github = \"flying-sheep\")),\nperson(given = \"Alex\",\nfamily = \"Wolf\",\nrole = \"ccp\",\nemail = \"f.alex.wolf@gmx.de\",\ncomment = c(ORCID = \"0000-0002-8760-7838\", github = \"falexwolf\")),\nperson(given = \"Isaac\",\nfamily = \"Virshup\",\nrole = \"ccp\",\ncomment = c(github = \"ivirshup\")),\nperson(given = \"Sergei\",\nfamily = \"Rybakov\",\nrole = \"ccp\",\ncomment = c(github = \"Koncopd\")),\nperson(given = \"Robrecht\",\nfamily = \"Cannoodt\",\nrole = c(\"aut\", \"ctb\", \"cre\", \"cph\"),\nemail = \"rcannood@gmail.com\",\ncomment = c(ORCID = \"0000-0003-3641-729X\", github = \"rcannood\")))","Description":"A 'reticulate' wrapper for the Python package 'anndata'.\nProvides a scalable way of keeping track of data and learned\nannotations. Used to read from and write to the h5ad file format.","License":"MIT + file LICENSE","URL":"https://anndata.dynverse.org, https://github.com/dynverse/anndata","BugReports":"https://github.com/dynverse/anndata/issues","Depends":"R (>= 3.5.0)","Imports":"assertthat, methods, R6, reticulate","Suggests":"Matrix, stats, testthat, knitr, rmarkdown","Encoding":"UTF-8","RoxygenNote":"7.1.1","Config/reticulate":"list( packages = list( list(package = \"anndata\") ) )","VignetteBuilder":"knitr","NeedsCompilation":"no","Packaged":"2021-03-28 10:17:48 UTC; rcannood","Author":"Philipp Angerer [ccp] (,\nflying-sheep),\nAlex Wolf [ccp] (, falexwolf),\nIsaac Virshup [ccp] (ivirshup),\nSergei Rybakov [ccp] (Koncopd),\nRobrecht Cannoodt [aut, ctb, cre, cph]\n(, rcannood)","Maintainer":"Robrecht Cannoodt ","Repository":"CRAN","Date/Publication":"2021-03-28 10:50:02 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/anndata_0.7.5.2.tar.gz","jsonAuthors":[{"name":"Philipp Angerer","email":"phil.angerer@gmail.com","maintainer":false},{"name":"Alex Wolf","email":"f.alex.wolf@gmx.de","maintainer":false},{"name":"Isaac Virshup","email":null,"maintainer":false},{"name":"Sergei Rybakov","email":null,"maintainer":false},{"name":"Robrecht Cannoodt","email":"rcannood@gmail.com","maintainer":true}],"readme":"\n[![CRAN](https://www.r-pkg.org/badges/version/anndata)](https://cran.r-project.org/package=anndata)\n[![Build\nstatus](https://github.com/dynverse/anndata/workflows/R-CMD-check/badge.svg)](https://github.com/dynverse/anndata/actions)\n\n# anndata for R\n\n[`anndata`](https://anndata.readthedocs.io/en/latest/) is a commonly\nused Python package for keeping track of data and learned annotations,\nand can be used to read from and write to the h5ad file format. It is\nalso the main data format used in the scanpy python package (Wolf,\nAngerer, and Theis 2018).\n\n![](https://raw.githubusercontent.com/dynverse/anndata/master/man/readme_files/anndata_for_r.png)\n\nHowever, using scanpy/anndata in R can be a major hassle. When trying to\nread an h5ad file, R users could approach this problem in one of two\nways. A) You could read in the file manually (since it’s an H5 file),\nbut this involves a lot of manual work and a lot of understanding on how\nthe h5ad and H5 file formats work (also, expect major headaches from\ncryptic hdf5r bugs). Or B) interact with scanpy and anndata through\nreticulate, but run into issues converting some of the python objects\ninto R.\n\nWe recently published\n[`anndata`](https://cran.r-project.org/package=anndata) on CRAN, which\nis a reticulate wrapper for the Python package – with some syntax\nsprinkled on top to make R users feel more at home.\n\nanndata for R is still under active development at\n[github.com/dynverse/anndata](https://github.com/dynverse/anndata). If\nyou encounter any issues, feel free to post an issue on GitHub!\n\n## Installation\n\nYou can install `anndata` for R from CRAN as follows:\n\n``` r\ninstall.packages(\"anndata\")\n```\n\nNormally, reticulate should take care of installing Miniconda and the\nPython anndata.\n\nIf not, try running:\n\n``` r\nreticulate::install_miniconda()\nanndata::install_anndata()\n```\n\n## Getting started\n\nThe API of anndata for R is very similar to its Python counterpart. Here\nis an example:\n\n``` r\nlibrary(anndata)\n```\n\n ## \n ## Attaching package: 'anndata'\n\n ## The following object is masked from 'package:readr':\n ## \n ## read_csv\n\n``` r\nad <- read_h5ad(\"example_formats/pbmc_1k_protein_v3_processed.h5ad\")\n\nad\n```\n\n ## AnnData object with n_obs × n_vars = 713 × 33538\n ## var: 'gene_ids', 'feature_types', 'genome', 'highly_variable', 'means', 'dispersions', 'dispersions_norm'\n ## uns: 'hvgParameters', 'normalizationParameters', 'pca', 'pcaParameters'\n ## obsm: 'X_pca'\n ## varm: 'PCs'\n\n``` r\nMatrix::rowMeans(ad$X[1:10,])\n```\n\n ## AAACCCAAGTGGTCAG-1 AAAGGTATCAACTACG-1 AAAGTCCAGCGTGTCC-1 AACACACTCAAGAGTA-1 \n ## 0.06499579 0.06385104 0.06102355 0.06739055 \n ## AACACACTCGACGAGA-1 AACAGGGCAGGAGGTT-1 AACAGGGCAGTGTATC-1 AACAGGGTCAGAATAG-1 \n ## 0.08891241 0.08648681 0.09318970 0.09140243 \n ## AACCTGAAGATGGTCG-1 AACGGGATCGTTATCT-1 \n ## 0.06664118 0.07866523\n\nSee `?anndata` for a full list of the functions provided by this\npackage. Check out any of the other vignettes by clicking any of the\nlinks below:\n\n- [Getting\n started](https://anndata.dynverse.org/articles/getting_started.html)\n- [Demo with\n scanpy](https://anndata.dynverse.org/articles/scanpy_demo.html)\n\n## Future work\n\nIn some cases, this package may still act more like a Python package\nrather than an R package. Some more helper functions and helper classes\nneed to be defined in order to fully encapsulate `AnnData()` objects.\nExamples are `ad$chunked_X(...)`, backed file modes, `read_zarr()` and\n`ad$write_zarr()`.\n\n## Latest changes\n\nCheck out `news(package = \"anndata\")` or [NEWS.md](NEWS.md) for a full\nlist of changes.\n\n\n\n### Recent changes in anndata 0.7.5.2\n\n- MINOR CHANGE: Add getters and setter for the internal python\n objects.\n\n- MINOR CHANGE: Alter how and when Python objects get converted to R\n and vice versa.\n\n- DOCUMENTATION: Documentation site is available at\n !\n\n- DOCUMENTATION: Added two basic vignettes.\n\n### Recent changes in anndata 0.7.5.1\n\n- MINOR CHANGE: Add wrapper classes for Raw and Layers objects.\n\n- MAJOR CHANGE: Calling `ad[..., ...]` now correctly returns a view of\n `ad` instead of returning a matrix.\n\n- TESTING: Extend tests based on `theislab/anndata` repository.\n\n## References\n\n

\n\n

\n\nWolf, F Alexander, Philipp Angerer, and Fabian J Theis. 2018. “SCANPY:\nLarge-Scale Single-Cell Gene Expression Data Analysis.” *Genome Biology*\n19 (February): 15. .\n\n

\n\n

","jobInfo":{"package":"anndata","version":"0.7.5.2","parsingStatus":"success","parserVersion":1,"parsedAt":"2021-09-10T12:30:05+0000"}}

Description

Usage

Arguments

Examples