Sjcount is a utility for fast quantification of splice junctions in RNA-seq data. It is annotation-agnostic and offset-aware. This version does count multisplits.

The goal of anpan is to consolidate statistical methods for strain analysis. This includes automated filtering of metagenomic functional profiles, testing genetic elements for association with outcomes, phylogenetic association testing, and pathway-level random effects models.

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 lets you read and write files in Generic Feature Format (GFF) with Biopython integration.

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

This package provides data structures, algorithms and educational resources for bioinformatics.

Samtools implements various utilities for post-processing nucleotide sequence alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.

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.

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

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.

This package is a library to enable flexible and scalable operations on genomic interval dataframes in Python. Bioframe enables access to a rich set of dataframe operations. Working in Python enables rapid visualization and iteration of genomic analyses. The philosophy underlying bioframe is to enable flexible operations. Instead of creating a function for every possible use-case, we encourage users to compose functions to achieve their goals.

Morpheus is a modeling and simulation environment for the study of multi-scale and multicellular systems.

BWA-Meth works for single-end reads and for paired-end reads from the directional protocol (most common). It uses the method employed by methylcoder and Bismark of in silico conversion of all C's to T's in both reference and reads. It recovers the original read (needed to tabulate methylation) by attaching it as a comment which BWA appends as a tag to the read. It performs favorably to existing aligners gauged by number of on and off-target reads for a capture method that targets CpG-rich region.

Implementation of the Smith-Waterman algorithm.

The HH-suite is a software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

muon is a multimodal omics Python framework.

This package provides Python bindings to the bwa mem aligner.

This package is a set of R functions for generating precise figures. This tool helps you to create clean markdown reports about what you just discovered with your analysis script.

This package is a collection of Perl, Python, and R scripts for manipulating 3C/4C/5C/Hi-C data.

CoolBox is a toolkit for visual analysis of genomics data. It aims to be highly compatible with the Python ecosystem, easy to use and highly customizable with a well-designed user interface. It can be used in various visualization situations, for example, to produce high-quality genome track plots or fetch common used genomic data files with a Python script or command line, interactively explore genomic data within Jupyter environment or web browser.

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.

This package provides tools for handling BAM, SAM, Tabix, bgzf, CRAM, CSIv1, CSIv2 and FAI files.

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

This package provides an implementation of chunked, compressed, N-dimensional arrays for R, Zarr specification version 2 (2024) <doi:10.5281/zenodo.11320255>.