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r-psd
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public |
Produces power spectral density estimates through iterative refinement of the optimal number of sine-tapers at each frequency. This optimization procedure is based on the method of Riedel and Sidorenko (1995), which minimizes the Mean Square Error (sum of variance and bias) at each frequency, but modified for computational stability. The same procedure can now be used to calculate the cross spectrum.
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2023-06-16 |
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macs3
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public |
Model Based Analysis for ChIP-Seq data
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2023-06-16 |
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r-dplyr
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public |
A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
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2023-06-16 |
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r-readr
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public |
The goal of 'readr' is to provide a fast and friendly way to read rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.
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2023-06-16 |
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r-tibble
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public |
Provides a 'tbl_df' class (the 'tibble') with stricter checking and better formatting than the traditional data frame.
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2023-06-16 |
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r-ggplot2
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public |
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.
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2023-06-16 |
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r-colorspace
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public |
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 graphical user interface) 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). Details can be found on the project web page at <https://colorspace.R-Forge.R-project.org/> and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, <doi:10.18637/jss.v096.i01>).
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2023-06-16 |
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r-memes
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public |
A seamless interface to the MEME Suite family of tools for motif analysis. 'memes' provides data aware utilities for using GRanges objects as entrypoints to motif analysis, data structures for examining & editing motif lists, and novel data visualizations. 'memes' functions and data structures are amenable to both base R and tidyverse workflows.
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2023-06-16 |
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bioconductor-universalmotif
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public |
Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.
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2023-06-16 |
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bioconductor-do.db
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public |
A set of annotation maps describing the entire Disease Ontology
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2023-06-16 |
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bioconductor-ensdb.hsapiens.v86
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public |
Ensembl based annotation package
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2023-06-16 |
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r-dichromat
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public |
Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness.
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2023-06-16 |
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r-lazyeval
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public |
An alternative approach to non-standard evaluation using formulas. Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.
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2023-06-16 |
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r-lattice
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public |
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.
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2023-06-16 |
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r-matrix
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public |
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.
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2023-06-16 |
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r-dbplyr
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public |
A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.
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2023-06-16 |
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r-assertthat
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public |
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.
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2023-06-16 |
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bioconductor-genomeinfodb
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public |
Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.
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2023-06-16 |
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r-httr
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public |
Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).
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2023-06-16 |
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r-stringr
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public |
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.
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2023-06-16 |
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r-hms
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public |
Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.
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2023-06-16 |
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r-xml
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public |
Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".
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2023-06-16 |
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r-crayon
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public |
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.
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2023-06-16 |
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bioconductor-biocgenerics
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public |
The package defines many S4 generic functions used in Bioconductor.
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2023-06-16 |
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r-memoise
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public |
Cache the results of a function so that when you call it again with the same arguments it returns the pre-computed value.
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2023-06-16 |
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bioconductor-annotationdbi
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public |
Implements a user-friendly interface for querying SQLite-based annotation data packages.
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2023-06-16 |
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r-bitops
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public |
Functions for bitwise operations on integer vectors.
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2023-06-16 |
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r-rcurl
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public |
A wrapper for 'libcurl' <https://curl.se/libcurl/> Provides functions to allow one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.
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2023-06-16 |
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r-cytoexplorer
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public |
An intuitive and interactive approach to analysing cytometry data in R. This package has been developed under ROpenSci gudelines to integrate conventional and cutting edge cytometry analysis tools under a unified open-source framework.
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2023-06-16 |
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r-gtools
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public |
Functions to assist in R programming, including: - assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse logit transformations ('logit', 'inv.logit'), - test if a value is missing, empty or contains only NA and NULL values ('invalid'), - manipulate R's .Last function ('addLast'), - define macros ('defmacro'), - detect odd and even integers ('odd', 'even'), - convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'), - perform a binary search ('binsearch'), - sort strings containing both numeric and character components ('mixedsort'), - create a factor variable from the quantiles of a continuous variable ('quantcut'), - enumerate permutations and combinations ('combinations', 'permutation'), - calculate and convert between fold-change and log-ratio ('foldchange', 'logratio2foldchange', 'foldchange2logratio'), - calculate probabilities and generate random numbers from Dirichlet distributions ('rdirichlet', 'ddirichlet'), - apply a function over adjacent subsets of a vector ('running'), - modify the TCP\_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of data frames, even if the column names don't match ('smartbind'), - generate significance stars from p-values ('stars.pval'), - convert characters to/from ASCII codes ('asc', 'chr'), - convert character vector to ASCII representation ('ASCIIfy'), - apply title capitalization rules to a character vector ('capwords').
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2023-06-16 |
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bioconductor-opencyto
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public |
This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.
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2023-06-16 |
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r-embedsom
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public |
Provides a smooth mapping of multidimensional points into low-dimensional space defined by a self-organizing map. Designed to work with 'FlowSOM' and flow-cytometry use-cases. See Kratochvil et al. (2019) <doi:10.1101/496869>.
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2023-06-16 |
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bioconductor-ncdfflow
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public |
Provides HDF5 storage based methods and functions for manipulation of flow cytometry data.
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2023-06-16 |
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bioconductor-flowworkspace
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public |
This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.
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2023-06-16 |
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bioconductor-flowcore
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public |
Provides S4 data structures and basic functions to deal with flow cytometry data.
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2023-06-16 |
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r-bh
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public |
Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided as C++ template code which is resolved entirely at compile-time without linking. This package aims to provide the most useful subset of Boost libraries for template use among CRAN packages. By placing these libraries in this package, we offer a more efficient distribution system for CRAN as replication of this code in the sources of other packages is avoided. As of release 1.75.0-0, the following Boost libraries are included: 'accumulators' 'algorithm' 'align' 'any' 'atomic' 'beast' 'bimap' 'bind' 'circular_buffer' 'compute' 'concept' 'config' 'container' 'date_time' 'detail' 'dynamic_bitset' 'exception' 'flyweight' 'foreach' 'functional' 'fusion' 'geometry' 'graph' 'heap' 'icl' 'integer' 'interprocess' 'intrusive' 'io' 'iostreams' 'iterator' 'math' 'move' 'mp11' 'mpl' 'multiprecision' 'numeric' 'pending' 'phoenix' 'polygon' 'preprocessor' 'propery_tree' 'random' 'range' 'scope_exit' 'smart_ptr' 'sort' 'spirit' 'tuple' 'type_traits' 'typeof' 'unordered' 'utility' 'uuid'.
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2023-06-16 |
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r-mass
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public |
Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).
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2023-06-16 |
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r-superheat
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public |
A system for generating extendable and customizable heatmaps for exploring complex datasets, including big data and data with multiple data types.
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2023-06-16 |
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r-magrittr
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public |
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."
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2023-06-16 |
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r-rodeo
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public |
This version of the package has only one function intended for external usage: Rodeo. It estimates how strongly each present cell type expresses different genes based on bulk expression data and cell type proportions of samples in the bulk data.
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2023-06-16 |
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r-flowassist
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public |
What the package does (one paragraph).
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2023-06-16 |
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r-dir.expiry
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public |
Implements an expiration system for access to versioned directories. Directories that have not been accessed by a registered function within a certain time frame are deleted. This aims to reduce disk usage by eliminating obsolete caches generated by old versions of packages.
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2023-06-16 |
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r-pavian
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public |
R package and Shiny app to visualize and analyze metagenomics classification results from Kraken, Centrifuge and MetaPhlAn.
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2023-06-16 |
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r-shinyfiletree
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public |
This creates a widget with a shiny file tree.
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2023-06-16 |
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r-sankeyd3
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public |
Creates 'D3' 'JavaScript' Sankey graphs from 'R'.
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2023-06-16 |
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r-scenic
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public |
SCENIC workflow
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2023-06-16 |
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r-scopeloomr
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public |
R package to build generic .loom files aligning with the default naming convention of the .loom format and to integrate other data types e.g.: regulons (SCENIC), clusters from Seurat, ... The package can also be used to extract data from .loom files.
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2023-06-16 |
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r-personograph
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public |
Visualizes treatment effects using person icons, similar to Cates (NNT) charts.
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2023-06-16 |
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r-goplot
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public |
Implementation of multilayered visualizations for enhanced graphical representation of functional analysis data. It combines and integrates omics data derived from expression and functional annotation enrichment analyses. Its plotting functions have been developed with an hierarchical structure in mind: starting from a general overview to identify the most enriched categories (modified bar plot, bubble plot) to a more detailed one displaying different types of relevant information for the molecules in a given set of categories (circle plot, chord plot, cluster plot, Venn diagram, heatmap).
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2023-06-16 |
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r-ggplotgui
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public |
Easily explore data by creating ggplots through a (shiny-)GUI. R-code to recreate graph provided.
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2023-06-16 |
