| r-seuratwrappers | 0.1.0 | SeuratWrappers is a collection of community-provided methods and extensions for Seurat, curated by the Satija Lab at NYGC. These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently. | Mar 25, 2025 | GPL-3 | file LICENSE |
| 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-pagoda2 | 0.1.0 | Single-cell RNA-seq Analysis | Mar 25, 2025 | GPL-3 |
| r-pkgconfig | 2.0.3 | Set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected. | Mar 25, 2025 | MIT + file LICENSE |
| r-magrittr | 1.5 | Provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. To quote Rene Magritte, "Ceci n'est pas un pipe." | Mar 25, 2025 | MIT + file LICENSE |
| r-rcpp | 1.0.2 | The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013, <doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018, <doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details. | Mar 25, 2025 | GPL (>= 2) |
| r-lattice | 0.20_38 | A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements. See ?Lattice for an introduction. | Mar 25, 2025 | GPL (>= 2) |
| r-rcpparmadillo | 0.9.700.2.0 | 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that Armadillo requires a fairly recent compiler; for the g++ family at least version 4.6.* is required. | Mar 25, 2025 | GPL (>= 2) |
| r-plyr | 1.8.4 | A set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics. The development of 'plyr' has been generously supported by 'Becton Dickinson'. | Mar 25, 2025 | MIT + file LICENSE |
| 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-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-mgcv | 1.8_29 | Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) <doi:10.1201/9781315370279> for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family. | Mar 25, 2025 | GPL (>= 2) |
| r-matrix | 1.2_17 | A rich hierarchy of matrix classes, including triangular, symmetric, and diagonal matrices, both dense and sparse and with pattern, logical and numeric entries. Numerous methods for and operations on these matrices, using 'LAPACK' and 'SuiteSparse' libraries. | Mar 25, 2025 | GPL (>= 2) | file LICENCE |
| r-mass | 7.3_51.4 | Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002). | Mar 25, 2025 | GPL-2 | GPL-3 |
| r-stringr | 1.4.0 | A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another. | Mar 25, 2025 | GPL-2 | file LICENSE |
| r-munsell | 0.5.0 | Provides easy access to, and manipulation of, the Munsell colours. Provides a mapping between Munsell's original notation (e.g. "5R 5/10") and hexadecimal strings suitable for use directly in R graphics. Also provides utilities to explore slices through the Munsell colour tree, to transform Munsell colours and display colour palettes. | Mar 25, 2025 | MIT + file LICENSE |
| r-irlba | 2.3.3 | Fast and memory efficient methods for truncated singular value decomposition and principal components analysis of large sparse and dense matrices. | Mar 25, 2025 | GPL-3 |
| 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-rcolorbrewer | 1.1_2 | Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org | Mar 25, 2025 | Apache License 2.0 |
| 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-utf8 | 1.1.4 | Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display. | Mar 25, 2025 | Apache License (== 2.0) | 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-viridislite | 0.3.0 | Implementation of the 'viridis' - the default -, 'magma', 'plasma', 'inferno', and 'cividis' color maps for 'R'. 'viridis', 'magma', 'plasma', and 'inferno' are ported from 'matplotlib' <http://matplotlib.org/>, a popular plotting library for 'python'. 'cividis', was developed by Jamie R. Nuñez and Sean M. Colby. These color maps are designed in such a way that they will analytically be perfectly perceptually-uniform, both in regular form and also when converted to black-and-white. They are also designed to be perceived by readers with the most common form of color blindness (all color maps in this package) and color vision deficiency ('cividis' only). This is the 'lite' version of the more complete 'viridis' package that can be found at <https://cran.r-project.org/package=viridis>. | Mar 25, 2025 | MIT + file LICENSE |
| r-stringi | 1.4.3 | Fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the 'ICU' (International Components for Unicode) library, the package provides 'R' users with platform-independent functions known to 'Java', 'Perl', 'Python', 'PHP', and 'Ruby' programmers. Available features include: pattern searching (e.g., with 'Java'-like regular expressions or the 'Unicode' collation algorithm), random string generation, case mapping, string transliteration, concatenation, Unicode normalization, date-time formatting and parsing, and many more. | Mar 25, 2025 | file LICENSE (FOSS) |
| 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 |
