This package provides a cross between a 2D density plot and a scatter plot, implemented as a ggplot2 geom. Points in the scatter plot are colored by the number of neighboring points. This is useful to visualize the 2D-distribution of points in case of overplotting.

Bars, in the present context, are lines above and below text that abut with the text. Barred roman numerals are sometimes found in publications. The package provides a function that prints barred roman numerals (converting Arabic numerals if necessary). The package also provides a predicate \ifnumeric.

This package provides a package for typesetting scholarly critical editions, replacing the established ledmac and eledmac packages. It supports indexing by page and by line numbers, and simple tabular- and array-style environments. The package is distributed with the related reledpar package.

The package adds a macro \rgcounts which displays the allocation status of the TeX registers. The display is written into the .log file as it is a bit verbose. An automatic call to \rgcounts is done at \begin{document} and \end{document}.

Markup allows the use of HTML syntax with in Common Lisp code. This has the advantage of being able to copy HTML snippets and have them instantly be functional, less double quotes than a s-expression approach, and designers will be able to understand the embedded HTML.

File::Remove::remove removes files and directories. It acts like /bin/rm, for the most part. Although unlink can be given a list of files, it will not remove directories; this module remedies that. It also accepts wildcards, * and ?, as arguments for file names.

This package provides the \setcounterref and \addtocounterref commands which use the section (or other) number from the reference as the value to put into the counter. It also provides \setcounterpageref and \addtocounterpageref that do the corresponding thing with the page reference of the label.

This package provides an alternative interface to Bioconductor annotation resources, in particular the gene identifier mapping functionality of the org packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the TxDb packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

This package includes size measurements, clutch observations, and blood isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins observed on islands in the Palmer Archipelago near Palmer Station, Antarctica. Data were collected and made available by Dr. Kristen Gorman and the Palmer Station Long Term Ecological Research (LTER) Program.

This gem provides the classes LinkHeader and LinkHeader::Link, which represent HTTP Link headers conforming to RFC 5988. Objects can be constructed from and converted to text or a JSON-friendly Array representation. They can also be used to generate corresponding HTML link elements.

Oedipus Lex is a lexer generator in the same family as Rexical and Rex. It is based primarily on generating code much like you would a hand-written lexer. It uses StrScanner within a multi-level case statement. As such, Oedipus matches on the first match, not the longest.

The ragged2e package defines new commands \Centering, \RaggedLeft, and \RaggedRight and new environments Center, FlushLeft, and FlushRight, which set ragged text and are easily configurable to allow hyphenation (the corresponding commands in LaTeX, all of whose names are lower-case, prevent hyphenation altogether).

This package contains a collection of trans-omics datasets generated using various sequencing technologies such as RNA-seq, Mass spectrometry and ChIP-seq. Modalities include the bulk profiling of the phosphoproteome, proteome, transcriptome and epigenome. Data reflects the timecourses of different developmental systems from the mouse or human.

This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.

This package provides utilities for processing and analyzing the files that are exported from a recorded Zoom meeting. This includes analyzing data captured through video cameras and microphones, the text-based chat, and meta-data. You can analyze aspects of the conversation among meeting participants and their emotional expressions throughout the meeting.

Syntax Tree is a suite of tools built on top of the internal CRuby parser. It provides the ability to generate a syntax tree from source, as well as the tools necessary to inspect and manipulate that syntax tree. It can be used to build formatters, linters, language servers, and more.

This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. It also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.

This is a package for saving Bioconductor data structures into file artifacts, and loading them back into memory. This is a more robust and portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Text::Hyphen is a Ruby library to hyphenate words in various languages using Ruby-fied versions of TeX hyphenation patterns. It will properly hyphenate various words according to the rules of the language the word is written in. The algorithm is based on that of the TeX typesetting system by Donald E. Knuth.

The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.

Last Resort is a special-purpose font intended as a user-friendly alternative to tofu symbols. It includes glyphs designed to allow users to recognize which Unicode block a character belongs to so they can identify what type of font to install to properly display text. Undefined code points and noncharacters are also represented.

This package provides a minor mode for interacting with a Julia REPL running inside Emacs. The julia process is started in an ANSI terminal (term), which allows text formatting and colors, and interaction with the help system and the debugger. It is recommended that you use this minor mode with the package emacs-julia-mode.

The rotpages package allows you to format documents where small sets of pages are rotated by 180 degrees and rearranged, so that they can be read by turning the printed copy upside-down. It was developed for collecting exercises and solutions: using the package, you can print the exercise text normally and the solutions rotated.

TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments. This facilitates easy extraction of methylation data for regions of interest across different tumour types and studies.