15 packages on CRAN
5 packages on GitHub
3 packages on Bioconductor
A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.
An implementation of interpreted string literals, inspired by Python's Literal String Interpolation <https://www.python.org/dev/peps/pep-0498/> and Docstrings <https://www.python.org/dev/peps/pep-0257/> and Julia's Triple-Quoted String Literals <https://docs.julialang.org/en/stable/manual/strings/#triple-quoted-string-literals>.
Cache the results of a function so that when you call it again with the same arguments it returns the pre-computed value.
Track and report code coverage for your package and (optionally) upload the results to a coverage service like 'Codecov' <http://codecov.io> or 'Coveralls' <http://coveralls.io>. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.
A friendly interface for the construction of regular expressions.
Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with 'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text' and 'Atom'.
An interface to the Gmail RESTful API. Allows access to your Gmail messages, threads, drafts and labels.
A framework to create Bootstrap <http://getbootstrap.com/> HTML reports from 'knitr' 'rmarkdown'.
Identifies potential target sequences for a given set of primers and generates taxonomically annotated phylogenetic trees with the predicted amplification products.
Provides a simple type annotation for R that is usable in scripts, in the R console and in packages. It is intended as a convention to allow other packages to use the type information to provide error checking, automatic documentation or optimizations.
Automatically install packages when they are missing.
Check if a package name is available to use.
An implementation of Interpreted String Literals (f-strings) for R.
Provides a simple interface to lookup and print R function definitions, including C and C++ compiled code from .Call, .C, .Internal and .External calls. Also lookup of S3 and S4 generics, including a simple dialog to print any or all of the loaded methods for the generic.
Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.
Provides R bindings to the 'Sundown' 'Markdown' rendering library (https://github.com/vmg/sundown). 'Markdown' is a plain-text formatting syntax that can be converted to 'XHTML' or other formats. See http://en.wikipedia.org/wiki/Markdown for more information about 'Markdown'.
Download and install R packages stored in 'GitHub', 'BitBucket', or plain 'subversion' or 'git' repositories. This package is a lightweight replacement of the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.
Tools to more conveniently perform tasks associated with add-on packages. pacman conveniently wraps library and package related functions and names them in an intuitive and consistent fashion. It seeks to combine functionality from lower level functions which can speed up workflow.
Convenient functions for moving files, deleting directories, and a variety of string operations that facilitate manipulating file names and extracting information from strings.
Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.
A set of tools for cleaning up, post-processing, adding packages to the repository, and for emailing people etc.
Declare your functions with argument checks, and 'argufy' will generate and add the checking code for you.
The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.