This package provides a lightweight interface to Stan <https://mc-stan.org>. The CmdStanR interface is an alternative to RStan that calls the command line interface for compilation and running algorithms instead of interfacing with C++ via Rcpp'.

This package provides an object for plotting GRanges, RleList, UCSC file formats, and ffTrack objects in multi-track panels.

A tiny C library for managing SOM (Self-Organizing Maps) neural networks.

This package provides Python bindings to the libBigWig library for accessing bigWig files.

This package provides necessary tools for the analysis of the genomic interaction data stored in .cool format. This collection of tools includes operations like compartment, insulation or peak calling.

The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process.

This package provides a collection of useful functions for working with DNA methylation micro-array data.

Samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.

This package builds on Seurat's Doheatmap function code to produce a heatmap from a Seurat object with multiple annotation bars.

This package contains the Battenberg R package for subclonal copy number estimation, as described by Nik-Zainal et al.

ReadWriter is a set of R functions to read and write files conveniently.

This is a Perl interface to the HTS library for DNA sequencing.

Exonerate is a generic tool for pairwise sequence comparison. It allows the alignment of sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.

BEDOPS is a suite of tools to address common questions raised in genomic studies---mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

BEDOPS provides tools that perform highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.

This is an R package to query and expand DisGeNET data, and to visualize the results within R framework. The disgenet2r package is designed to retrieve data from DisGeNET v6.0 (Jan, 2019).

CLIPper is a tool to define peaks in CLIP-seq datasets.

The alignment module of BioJava provides an API that contains

• implementations of dynamic programming algorithms for sequence alignment;

• reading and writing of popular alignment file formats;

• a single-, or multi- threaded multiple sequence alignment algorithm.

Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools.

Screed parses FASTA and FASTQ files and generates databases. Values such as sequence name, sequence description, sequence quality and the sequence itself can be retrieved from these databases.

MACS is an implementation of a ChIP-Seq analysis algorithm for identifying transcript factor binding sites named Model-based Analysis of ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and it improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.

Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and a command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.

This is a package providing efficient operations for single cell ATAC-seq fragments and RNA counts matrices. It is interoperable with standard file formats, and introduces efficient bit-packed formats that allow large storage savings and increased read speeds.

This package provides a Python client for BioThings API services.

This package provides Python bindings for spoa, a C++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences