Bioparser is a C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.

FAN-C provides a pipeline for analysing Hi-C data starting at mapped paired-end sequencing reads.

This package provides a converter between .hic files (from juicer) and single-resolution or multi-resolution .cool files (for cooler). Both hic and cool files describe Hi-C contact matrices.

This package provides string parsing functionalities for generating plotnames, filenames and paths.

This package provides different statistical methods to extract biological activities from omics data within a unified framework.

HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover the whole genome. These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons.

This package is a rasterization preprocessing framework that aggregates cellular information into spatial pixels to reduce resource requirements for spatial omics data analysis. SEraster reduces the number of points in spatial omics datasets for downstream analysis through a process of rasterization where single cells gene expression or cell-type labels are aggregated into equally sized pixels based on a user-defined resolution. SEraster can be incorporated with other packages to conduct downstream analyses for spatial omics datasets, such as detecting spatially variable genes.

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the jellyfish dump command, or queried for specific k-mers with jellyfish query.

This package provides a library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.8+).

This package is a Python wrapper for Aaron Quinlan's BEDtools programs, which are widely used for genomic interval manipulation or "genome algebra". pybedtools extends BEDTools by offering feature-level manipulations from with Python.

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).

The NCBI-VDB library implements a highly compressed columnar data warehousing engine that is most often used to store genetic information. Databases are stored in a portable image within the file system, and can be accessed/downloaded on demand across HTTP.

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.

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.

uGet is portable download manager with GTK+ interface supporting HTTP, HTTPS, BitTorrent and Metalink, supporting multi-connection downloads, download scheduling, download rate limiting.

Tremc is a console client, with a curses interface, for the Transmission BitTorrent daemon.

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

mktorrent is a simple command-line utility to create BitTorrent metainfo files, often known simply as torrents, from both single files and whole directories. It can add multiple trackers and web seed URLs, and set the private flag to disallow advertisement through the distributed hash table (DHT) and Peer Exchange. Hashing is multi-threaded and will take advantage of multiple processor cores where possible.

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

qBittorrent is a BitTorrent client programmed in C++/Qt that uses libtorrent (sometimes called libtorrent-rasterbar) by Arvid Norberg.

It aims to be a good alternative to all other BitTorrent clients out there. qBittorrent is fast, stable and provides unicode support as well as many features.

qBittorrent is a BitTorrent client programmed in C++/Qt that uses libtorrent (sometimes called libtorrent-rasterbar) by Arvid Norberg.

It aims to be a good alternative to all other BitTorrent clients out there. qBittorrent is fast, stable and provides unicode support as well as many features.

LibTorrent is a BitTorrent library used by and developed in parallel with the BitTorrent client rtorrent. It is written in C++ with emphasis on speed and efficiency.

libtorrent-rasterbar is a feature-complete C++ BitTorrent implementation focusing on efficiency and scalability. It runs on embedded devices as well as desktops.

transmission-remote-gtk is a GTK client for remote management of the Transmission BitTorrent client, using its HTTP RPC protocol.