This R package lets you estimate signatures of mutational processes and their activities on mutation count data. Starting from a set of single-nucleotide variants (SNVs), it allows both estimation of the exposure of samples to predefined mutational signatures (including whether the signatures are present at all), and identification of signatures de novo from the mutation counts.

Cell2cell is a Python library for cell communication analysis. This is a method to calculate, visualize and analyze communication between cell types. Cell2cell is suitable for single-cell RNA sequencing (scRNA-seq) data.

python-cwlformat is a specification and a reference implementation for a very opinionated CWL code formatter. It outputs CWL in a standardized YAML format.

MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate parameters of gene regulation, providing a quantitative summary of the temporal relationship between epigenomic and transcriptomic changes.

BioPerl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. These objects not only do what they are advertised to do in the documentation, but they also interact - Alignment objects are made from the Sequence objects, Sequence objects have access to Annotation and SeqFeature objects and databases, Blast objects can be converted to Alignment objects, and so on. This means that the objects provide a coordinated and extensible framework to do computational biology.

Biosoup is a C++ collection of header-only data structures used for storage and logging in bioinformatics tools.

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.

BamTools provides both a C++ API and a command-line toolkit for handling BAM files.

Proteinortho is a tool to detect orthologous genes across different species. For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at once.

The data within this package is a panel of four samples, each with 3000 cells. There are two samples which are bone marrow (BM), and two samples which are cord blood (CB).

Piranha is a peak-caller for genomic data produced by CLIP-seq and RIP-seq experiments. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process.

DendroPy is a library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs.

TADbit is a complete Python library to deal with all steps to analyze, model, and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models.

Ngesh is a Python library and CLI tool for simulating phylogenetic trees and data. It is intended for benchmarking phylogenetic methods, especially in historical linguistics andstemmatology. The generation of stochastic phylogenetic trees also goes by the name simulationmethods for phylogenetic trees, synthetic data generation, or just phylogenetic tree simulation.

Fxtract extracts sequences from a protein or nucleotide fastx (FASTA or FASTQ) file given a subsequence. It uses a simple substring search for basic tasks but can change to using POSIX regular expressions, PCRE, hash lookups or multi-pattern searching as required. By default fxtract looks in the sequence of each record but can also be told to look in the header, comment or quality sections.

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.

This package provides an automated pipeline for spatial mapping of unique transcripts.

Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads.

Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. Its main features are:

• Bisulfite mapping and methylation calling in one single step

• Supports single-end and paired-end read alignments

• Supports ungapped and gapped alignments

• Alignment seed length, number of mismatches etc are adjustable

• Output discriminates between cytosine methylation in CpG, CHG and CHH context

Biopython is a set of tools for biological computation including parsers for bioinformatics files into Python data structures; interfaces to common bioinformatics programs; a standard sequence class and tools for performing common operations on them; code to perform data classification; code for dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.

Salad is a schema language for describing JSON or YAML structured linked data documents. Salad schema describes rules for preprocessing, structural validation, and hyperlink checking for documents described by a Salad schema. Salad supports rich data modeling with inheritance, template specialization, object identifiers, object references, documentation generation, code generation, and transformation to RDF. Salad provides a bridge between document and record oriented data modeling and the Semantic Web.

python-scanrbp is a Python package that provides the scanRBP tool that loads RNA-protein binding motif PWM and computes the log-odds scores for all the loaded RBPs across a given genomic sequence and draws a heatmap of the scores.

This package offers a quick and straight-forward way to explore and perform basic analysis of single cell sequencing data coming from droplet sequencing. It has been particularly tailored for Drop-seq.