Megahit is a fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.

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.

The metacells package implements the improved metacell algorithm for single-cell RNA sequencing (scRNA-seq) data analysis within the scipy framework, and projection algorithm based on it. The original metacell algorithm was implemented in R. The Python package contains various algorithmic improvements and is scalable for larger data sets (millions of cells).

Mosaicatcher counts Strand-seq reads and classifies strand states of each chromosome in each cell using a Hidden Markov Model.

This R package provides additional capabilities and speed for GenomicRanges operations.

This package provides a VCF parser for Python.

This package stores motif collections as lists of position frequency matrix (PWMatrixList) objects provided by the TFBSTools package for use in R with packages like motifmatchr or chromVAR.

This package provides accelerated functions for the CIRI toolkit. It also provides the ccs executable to scan for circular consensus sequences.

This package provides necessary tools for the analysis of the genomic interaction data stored in .cool format. This collection of tools includes operations like compartment, insulation or peak calling.

The ccwl is a concise syntax to express CWL workflows. ccwl is a compiler to generate CWL workflows from concise descriptions in ccwl. It is implemented as an EDSL in the Scheme programming language.

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.

Megadepth is an efficient tool for extracting coverage related information from RNA and DNA-seq BAM and BigWig files. It supports reading whole-genome coverage from BAM files and writing either indexed TSV or BigWig files, as well as efficient region coverage summary over intervals from both types of files.

This is a Ligand-Receptor inference framework. The framework enables the use of any LR method with any resources.

Harmony is an algorithm for integrating multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

QTLtools is a tool set for molecular QTL discovery and analysis. It allows going from the raw genetic sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps.

This package provides a set of R functions to parse markdown and other generic helpers.

Several studies focus on the inference of developmental and response trajectories from single cell RNA-Seq (scRNA-Seq) data. A number of computational methods, often referred to as pseudo-time ordering, have been developed for this task. CRISPR has also been used to reconstruct lineage trees by inserting random mutations. The tbsp package implements an alternative method to detect significant, cell type specific sequence mutations from scRNA-Seq data.

Cooler is a support library for a sparse, compressed, binary persistent storage format, called cool, used to store genomic interaction data, such as Hi-C contact matrices.

Bíogo is a bioinformatics library for the Go language.

Express Beta Diversity (EBD) calculates ecological beta diversity (dissimilarity) measures between biological communities. EBD implements a variety of diversity measures including those that make use of phylogenetic similarity of community members.

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 package provides R miscellaneous utilities for basic data manipulation, debugging, visualization, lsf management, and common mskilab tasks.

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).

Ribotaper is a method for defining translated open reading frames (ORFs) using ribosome profiling (ribo-seq) data. This package provides the Ribotaper pipeline.