This package provides a fast, JVM-free toolkit for removing duplicate reads from BAM/CRAM. It handles the two major kinds of duplication event in sequencing data, each a faithful, independent port of the standard reference tool, with the performance-critical inner loops accelerated in Cython.

This package implements the custom CRAM codecs used for "EXTERNAL" block types. These consist of two variants of the rANS codec (8-bit and 16-bit renormalisation, with run-length encoding and bit-packing also supported in the latter), a dynamic arithmetic coder, and custom codecs for name/ID compression and quality score compression derived from fqzcomp.

METAL is a tool for meta-analysis genomewide association scans. METAL can combine either test statistics and standard errors or p-values across studies (taking sample size and direction of effect into account). METAL analysis is a convenient alternative to a direct analysis of merged data from multiple studies. It is especially appropriate when data from the individual studies cannot be analyzed together because of differences in ethnicity, phenotype distribution, gender or constraints in sharing of individual level data imposed. Meta-analysis results in little or no loss of efficiency compared to analysis of a combined dataset including data from all individual studies.

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This library provides sequence-related modules.

This package is intended to help users to efficiently analyze genomic data resulting from various experiments.

The Maxprobes package collects cross-reactive probes of Illumina methylation array 450K and EPIC/850K.

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). In addition to using one global graph FM (GFM) index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes, combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

This package provides Python bindings to the UCSC Big Binary (bigWig/bigBed) file library. This provides read-level access to local and remote bigWig and bigBed files but no write capabilitites. The main feature is fast retrieval of range queries into numpy arrays.

This package provides a set of functions to parse and open (search query) links to genomics related and other websites for R. Useful when you want to explore e.g.: the function of a set of differentially expressed genes.

This R tool infers, visualizes, and analyzes cell-cell communication networks. It supports scRNA-seq and spatially resolved transcriptomics data.

CodeAndRoll2 is a set of more than 130 productivity functions. These functions are used by MarkdownReports, ggExpress, and SeuratUtils.

This package provides a Python module creating/accessing GTF-based interval trees with associated meta-data. It is primarily used by the deeptools package.

The package reads phylogenetic data in the phyloXML format. It also includes functions for writing data in this format.

pySCENIC is a Python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

This package offers Cython bindings and a Python interface for Prodigal. Prodigal is an ORF finder designed for both genomes and metagenomes.

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. It is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

ShoRAH is a project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools provide error correction, haplotype reconstruction and estimation of the frequency of the different genetic variants present in a mixed sample.

This package provides extra utility functions to perform common tasks in the analysis of omics data, leveraging and enhancing features provided by Bioconductor packages.

FLASH (Fast Length Adjustment of SHort reads) is a tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.

Cyvcf2 is a Cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.

SeqGL is a group lasso based algorithm to extract transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. This package presents a method which uses group lasso to discriminate between bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.

GNU Bison is a general-purpose parser generator. It can build a deterministic or generalized LR parser from an annotated, context-free grammar. It is versatile enough to have many applications, from parsers for simple tools through complex programming languages.

Bison also provides an implementation of yacc, as specified by POSIX.

Stig is a TUI and CLI client for the BitTorrent client Transmission.

qBittorrent Enhanced is a bittorrent client based on qBittorrent with the following features:

• Auto Ban Xunlei, QQ, Baidu, Xfplay, DLBT and Offline downloader

• Auto Ban Unknown Peer from China Option (Default: OFF)

• Auto Update Public Trackers List (Default: OFF)

• Auto Ban BitTorrent Media Player Peer Option (Default: OFF)

• Peer whitelist/blacklist