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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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2025-03-25 |
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macs3
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public |
Model Based Analysis for ChIP-Seq data
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2025-03-25 |
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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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2025-03-25 |
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r-readr
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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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2025-03-25 |
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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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2025-03-25 |
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r-ggplot2
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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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2025-03-25 |
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r-colorspace
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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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2025-03-25 |
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r-memes
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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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2025-03-25 |
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bioconductor-universalmotif
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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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2025-03-25 |
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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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2025-03-25 |
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bioconductor-ensdb.hsapiens.v86
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Ensembl based annotation package
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2025-03-25 |
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r-dichromat
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Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness.
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2025-03-25 |
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r-lazyeval
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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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2025-03-25 |
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r-lattice
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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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2025-03-25 |
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r-matrix
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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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2025-03-25 |
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r-dbplyr
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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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2025-03-25 |
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r-assertthat
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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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2025-03-25 |
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bioconductor-genomeinfodb
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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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2025-03-25 |
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r-httr
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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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2025-03-25 |
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r-stringr
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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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2025-03-25 |
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r-hms
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Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.
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2025-03-25 |
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r-xml
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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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2025-03-25 |
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r-crayon
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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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2025-03-25 |
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bioconductor-biocgenerics
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The package defines many S4 generic functions used in Bioconductor.
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2025-03-25 |
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r-memoise
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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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2025-03-25 |
