SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies.

bio2zarr efficiently converts common bioinformatics formats to Zarr format.

Tools:

• vcf2zarr converts VCF data to VCF Zarr format;

• plink2zarr converts PLINK 1.0 data to VCF Zarr format;

• tskit2zarr converts tskit data into VCF Zarr format;

• vcfpartition is a utility to split an input VCF into a given number of partitions;

• zipzarr is a utility for zipping/unzipping Zarr directory stores.

SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies.

Kastore is a simple storage format mapping keys to numerical arrays in a write-once-read-many file store.

This package provides a fast interval tree-like implementation in C, wrapped for the Python ecosystem.

msprime is a population genetics simulator based on tskit. Msprime can simulate random ancestral histories for a sample of individuals (consistent with a given demographic model) under a range of different models and evolutionary processes. Msprime can also simulate mutations on a given ancestral history (which can be produced by msprime or other programs supporting tskit) under a variety of genome sequence evolution models.

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

This package provides gzip-like compression for tskit tree sequences. Compression is lossless for supported tskit tree sequences.

The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest.

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

This package provides utilities for comparing ARGs represented as tree sequences. It includes tooling to quantify similarities and differences between ARG topologies, haplotype paths, and related structures.

diemPy is a computational tool designed to polarize genomic data for hybrid zone analysis. The package implements an expectation-maximization (EM) algorithm to determine the optimal polarization of genetic markers, enabling researchers to identify and analyze patterns of introgression and hybridization in genomic datasets.

This package provides in uncompressed version of the gnomAD structural variant sites.

hiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains, like HK27me3. The input data can be in BAM format, or in a tab-delimited 'reads per bin' format described below. The output is a BED formatted file the lists the enriched domains and their posterior probabilities.

SeqAn is a C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It contains algorithms and data structures for string representation and their manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.

SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.

Build contrasts for models defined with formulaic.

This package provides a subset of the Regulatory Sequence Analysis Tools (RSAT).

tstrait is a Python package to simulate quantitative traits from a given tree sequence.

This package contains a collection of bioinformatics data structures and algorithms. It provides I/O classes, bitio classes, text indexing classes and BAM sequence alignment functionality.

This package contains functions to extract information from Oxford Nanopore sequencing data and alignments.