| r-assertthat | 0.2.1 | An extension to stopifnot() that makes it easy to declare the pre and post conditions that you code should satisfy, while also producing friendly error messages so that your users know what's gone wrong. | Mar 25, 2025 | GPL-3 |
| r-backports | 1.1.4 | Functions introduced or changed since R v3.0.0 are re-implemented in this package. The backports are conditionally exported in order to let R resolve the function name to either the implemented backport, or the respective base version, if available. Package developers can make use of new functions or arguments by selectively importing specific backports to support older installations. | Mar 25, 2025 | GPL-2 |
| r-biocgenerics | 0.31.6 | The package defines S4 generic functions used in Bioconductor. | Mar 25, 2025 | Artistic-2.0 |
| r-busparse | 0.99.25 | The kallisto | bustools pipeline is a fast and modular set of tools to convert single cell RNA-seq reads in fastq files into gene count or transcript compatibility counts (TCC) matrices for downstream analysis. Central to this pipeline is the barcode, UMI, and set (BUS) file format. This package serves the following purposes: First, this package allows users to manipulate BUS format files as data frames in R and then convert them into gene count or TCC matrices. Furthermore, since R and Rcpp code is easier to handle than pure C++ code, users are encouraged to tweak the source code of this package to experiment with new uses of BUS format and different ways to convert the BUS file into gene count matrix. Second, this package can conveniently generate files required to generate gene count matrices for spliced and unspliced transcripts for RNA velocity. Third, this package implements utility functions to get transcripts and associated genes required to convert BUS files to gene count matrices, to write the transcript to gene information in the format required by bustools, and to read output of bustools into R as sparses matrices. | Mar 25, 2025 | BSD_2_clause + file LICENSE |
| r-cluster | 2.1.0 | Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding Groups in Data". | Mar 25, 2025 | GPL (>= 2) |
| r-colorspace | 1.4_1 | Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny GUI) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). | Mar 25, 2025 | BSD_3_clause + file LICENSE |
| r-conos | 1.1.2 | Wire together large collections of single-cell RNA-seq datasets. The package focuses on uniform mapping of homologous cell types across heterogeneous sample collections. For instance, a collection of dozens of peripheral blood samples from cancer patients, combined with dozens of controls. And perhaps also including samples of a related tissue, such as lymph nodes. | Mar 25, 2025 | GPL3 |
| r-cowplot | 1.0.0 | Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization. | Mar 25, 2025 | GPL-2 |
| r-crayon | 1.3.4 | Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project. | Mar 25, 2025 | MIT + file LICENSE |
| r-dabestr | 0.2.2 | Data Analysis using Bootstrap-Coupled ESTimation. Estimation statistics is a simple framework that avoids the pitfalls of significance testing. It uses familiar statistical concepts: means, mean differences, and error bars. More importantly, it focuses on the effect size of one's experiment/intervention, as opposed to a false dichotomy engendered by P values. An estimation plot has two key features: 1. It presents all datapoints as a swarmplot, which orders each point to display the underlying distribution. 2. It presents the effect size as a bootstrap 95% confidence interval on a separate but aligned axes. Estimation plots are introduced in Ho et al., Nature Methods 2019, 1548-7105. <doi:10.1038/s41592-019-0470-3>. The free-to-view PDF is located at <https://rdcu.be/bHhJ4>. | Mar 25, 2025 | file LICENSE |
| r-digest | 0.6.21 | Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash' and 'spookyhash' algorithms) permitting easy comparison of R language objects, as well as functions such as'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used. | Mar 25, 2025 | GPL (>= 2) |
| r-dofuture | 0.2.0 | Provides a '%dopar%' adaptor such that any type of futures can be used as backends for the 'foreach' framework. | Mar 25, 2025 | LGPL (>= 2.1) |
| r-dosnow | 1.0.18 | Provides a parallel backend for the %dopar% function using the snow package of Tierney, Rossini, Li, and Sevcikova. | Mar 25, 2025 | GPL-2 |
| r-ellipsis | 0.3.0 | The ellipsis is a powerful tool for extending functions. Unfortunately this power comes at a cost: misspelled arguments will be silently ignored. The ellipsis package provides a collection of functions to catch problems and alert the user. | Mar 25, 2025 | GPL-3 |
| r-fansi | 0.4.0 | Counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences. | Mar 25, 2025 | GPL (>= 2) |
| r-fnn | 1.1.3 | Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications including KNN classification, regression and information measures are implemented. | Mar 25, 2025 | GPL (>= 2) |
| r-foreach | 1.4.7 | Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel. | Mar 25, 2025 | Apache License (== 2.0) |
| r-future | 1.11.1.1 | The purpose of this package is to provide a lightweight and unified Future API for sequential and parallel processing of R expression via futures. The simplest way to evaluate an expression in parallel is to use `x %<-% { expression }` with `plan(multiprocess)`. This package implements sequential, multicore, multisession, and cluster futures. With these, R expressions can be evaluated on the local machine, in parallel a set of local machines, or distributed on a mix of local and remote machines. Extensions to this package implement additional backends for processing futures via compute cluster schedulers etc. Because of its unified API, there is no need to modify any code in order switch from sequential on the local machine to, say, distributed processing on a remote compute cluster. Another strength of this package is that global variables and functions are automatically identified and exported as needed, making it straightforward to tweak existing code to make use of futures. | Mar 25, 2025 | LGPL (>= 2.1) |
| r-ggplot2 | 3.2.1 | A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details. | Mar 25, 2025 | GPL-2 | file LICENSE |
| r-ggrepel | 0.8.1 | Provides text and label geoms for 'ggplot2' that help to avoid overlapping text labels. Labels repel away from each other and away from the data points. | Mar 25, 2025 | GPL-3 | file LICENSE |
| r-glue | 1.3.1 | 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>. | Mar 25, 2025 | MIT + file LICENSE |
| r-gtable | 0.3.0 | Tools to make it easier to work with "tables" of 'grobs'. The 'gtable' package defines a 'gtable' grob class that specifies a grid along with a list of grobs and their placement in the grid. Further the package makes it easy to manipulate and combine 'gtable' objects so that complex compositions can be build up sequentially. | Mar 25, 2025 | GPL-2 |
| r-harmony | 1.0 | Implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al <doi.org/10.1101/461954>. Package includes a standalone Harmony function and interfaces to external frameworks. | Mar 25, 2025 | GPL-3 + file LICENSE |
| r-hmisc | 4.2_0 | Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, and recoding variables. | Mar 25, 2025 | GPL (>= 2) |
| r-ica | 1.0_2 | Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE). | Mar 25, 2025 | GPL (>= 2) |
