WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.

WebLogo can create output in several common graphics' formats, including the bitmap formats GIF and PNG, suitable for on-screen display, and the vector formats EPS and PDF, more suitable for printing, publication, and further editing. Additional graphics options include bitmap resolution, titles, optional axis, and axis labels, antialiasing, error bars, and alternative symbol formats.

A sequence logo is a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. The width of the stack is proportional to the fraction of valid symbols in that position.

This package provides an implementation of the BITS (Binary Interval Search) algorithm, an approach to interval set intersection. It is especially suited for the comparison of diverse genomic datasets and the exploration of large datasets of genome intervals (e.g. genes, sequence alignments).

python-cwl-utils provides python utilities and autogenerated classes for loading and parsing CWL v1.0, CWL v1.1, and CWL v1.2 documents.

This package contains a multicore Barnes-Hut implementation of the t-SNE algorithm. The implementation is described here: http://lvdmaaten.github.io/publications/papers/JMLR_2014.pdf.

The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.

CPAT is a method to distinguish coding and noncoding RNA by using a logistic regression model based on four pure sequence-based, linguistic features: ORF size, ORF coverage, Ficket TESTCODE, and Hexamer usage bias. Linguistic features based method does not require other genomes or protein databases to perform alignment and is more robust. Because it is alignment-free, it runs much faster and also easier to use.

This package provides TagGD barcode demultiplexing utilities for Spatial Transcriptomics data.

Change-O is a collection of tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin (Ig) sequences, and reconstructing germline sequences.

This package provides graphical user interfaces to organize and visualize Nanopore sequencing data.

Python-airr provides a library by the AIRR community to for describing, reporting, storing, and sharing adaptive immune receptor repertoire (AIRR) data, such as sequences of antibodies and T cell receptors (TCRs).

DIAMOND is a BLAST-compatible local aligner for mapping protein and translated DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings.

Bowtie 2 is a fast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

This package implements a bioinformatics algorithm for demultiplexing multiplexed single cell datasets. It is built on a statistical model of tag read counts derived from the physical mechanism of tag cross-contamination.

This package is designed to streamline scATAC analyses in R.

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.

Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments.

Sylamer is a system for finding significantly over or under-represented words in sequences according to a sorted gene list. Typically it is used to find significant enrichment or depletion of microRNA or siRNA seed sequences from microarray expression data. Sylamer is extremely fast and can be applied to genome-wide datasets with ease. Results are plotted in terms of a significance landscape plot. These plots show significance profiles for each word studied across the sorted genelist.

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.

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.

Deluge contains the common features to BitTorrent clients such as Protocol Encryption, DHT, Local Peer Discovery (LSD), Peer Exchange (PEX), UPnP, NAT-PMP, Proxy support, Web seeds, global and per-torrent speed limits. Deluge heavily utilises the libtorrent library. It is designed to run as both a normal standalone desktop application and as a client-server.

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.

Aria2 is a lightweight, multi-protocol & multi-source command-line download utility. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink. Aria2 can be manipulated via built-in JSON-RPC and XML-RPC interfaces.

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.