This library contains the genomics components of the Bio++ sequence library. It is part of the Bio++ project.

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.

This package infers, visualizes and analyzes the cell-cell communication networks from scRNA-seq data.

Savvy is the official C++ interface for the SAV file format and offers seamless support for BCF and VCF files.

PiGX RNAseq is an analysis pipeline for preprocessing and reporting for RNA sequencing experiments. It is easy to use and produces high quality reports. The inputs are reads files from the sequencing experiment, and a configuration file which describes the experiment. In addition to quality control of the experiment, the pipeline produces a differential expression report comparing samples in an easily configurable manner.

Forester is a collection of Java libraries for phylogenomics and evolutionary biology research. It includes support for reading, writing, and exporting phylogenetic trees.

This package facilitates the analysis of single-cell RNA-seq UMI matrices. It does this by computing partitions of a cell similarity graph into small homogeneous groups of cells, which are defined as metacells (MCs). The derived MCs are then used for building different representations of the data, allowing matrix or 2D graph visualization forming a basis for analysis of cell types, subtypes, transcriptional gradients,cell-cycle variation, gene modules and their regulatory models and more.

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.

This is a package for normalizing Hi-C contact counts efficiently.

Sleuth is a program for differential analysis of RNA-Seq data. It makes use of quantification uncertainty estimates obtained via Kallisto for accurate differential analysis of isoforms or genes, allows testing in the context of experiments with complex designs, and supports interactive exploratory data analysis via sleuth live.

An ORF caller finds stretches of DNA that, when translated, are not interrupted by stop codons. OrfM finds and prints these ORFs.

The package graph implements graph manipulation functions.

MuSiC is a deconvolution method that utilizes cross-subject scRNA-seq to estimate cell type proportions in bulk RNA-seq data.

This package provides Shiny apps for interactive exploration of single-cell data.

This package provides an R API and htmlwidget facilitating interactive visualization of spatial single-cell data with Vitessce. The R API contains classes and functions for loading single-cell data stored in compatible on-disk formats. The htmlwidget is a wrapper around the Vitessce JavaScript library and can be used in the Viewer tab of RStudio or Shiny apps.

Ngless is a domain-specific language for next-generation sequencing (NGS) data processing.

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This library provides population genetics-related modules.

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be optionally compressed by gzip.

CrossMap is a program for conversion of genome coordinates or annotation files between different genome assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.

VoltRon is a novel spatial omic analysis toolbox for multi-omics integration using spatial image registration. VoltRon is capable of analyzing multiple types and modalities of spatially-aware datasets. VoltRon visualizes and analyzes regions of interests (ROIs), spots, cells and even molecules.

This package provides a Python package for reading raw fcs files

CLIPper is a tool to define peaks in CLIP-seq datasets.

Cyvcf2 is a Cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.

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