MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It contains modules for a large number of common bioinformatics tools.

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.

This package provides a companion annotation file to the IlluminaHumanMethylationEPICmanifest package based on the same annotation 1.0B5.

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

This package implements bindings for zarr store that are compatible with Bioconductor S4 data structures, namely the DataFrame and DelayedArray. This allows Zarr-backed data to be easily used as data frames with arbitrary sets of columns.

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

Circe is a Python package for inferring co-accessibility networks from single-cell ATAC-seq data, using skggm for the graphical lasso and python-scanpy for data processing.

SQUID is Sean Eddy's personal library of C functions and utility programs for sequence analysis.

BayesPrism includes deconvolution and embedding learning modules. The deconvolution module models a prior from cell type-specific expression profiles from scRNA-seq to jointly estimate the posterior distribution of cell type composition and cell type-specific gene expression from bulk RNA-seq expression of tumor samples. The embedding learning module uses Expectation-maximization (EM) to approximate the tumor expression using a linear combination of malignant gene programs while conditional on the inferred expression and fraction of non-malignant cells estimated by the deconvolution module.

A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. In order to use the program, the user submits a sequence in FASTA format. The output consists of two files: a repeat table file and an alignment file. Submitted sequences may be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 bases are detected.

The Shaman package implements functions for resampling Hi-C matrices in order to generate expected contact distributions given constraints on marginal coverage and contact-distance probability distributions. The package also provides support for visualizing normalized matrices and statistical analysis of contact distributions around selected landmarks.

R-scape discovers RNA secondary structure consensus elements. These elements include riboswitches and ribozymes. It utilizes probabilistic modeling of sequence alignments, explicitly considering folding dependencies. The tool enables the de novo search for new structural elements and facilitates comparative analysis of known RNA families.

This package lets you read and write the PLINK BED format, simply and efficiently.

This is a package that lets you process UMI-4C data from scratch to produce nice plots.

This package performs a fast Wilcoxon rank sum test and auROC analysis.

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.

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.

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

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 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

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

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.