599 Open source projects that are alternatives of or similar to Plip

A DSL for data-driven computational pipelines

A robust and fast clustering method for amplicon-based studies

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

Demonstrating best practices for bioinformatics command line tools

Structural variant toolkit for VCFs

UGENE is free open-source cross-platform bioinformatics software

Race and ethnicity Imputation from Disease history with Deep LEarning

Application for making ENCODE Blacklists

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

Automatic Differentiation Library for Computational and Mathematical Engineering

pymzML - an interface between Python and mzML Mass spectrometry Files

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

An efficient FASTQ manipulation suite

Antimicrobial Resistance Identification By Assembly

Workflow engine for exploration of simulation models using high throughput computing

Open-source software for volunteer computing and grid computing.

Benchmarking programming languages/implementations for common tasks in Bioinformatics

Bioinformatics library for .NET

Linear algebra, eigenvalues, FFT, Bessel, elliptic, orthogonal polys, geometry, NURBS, numerical quadrature, 3D transfinite interpolation, random numbers, Mersenne twister, probability distributions, optimisation, differential equations.

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

A Practical and Efficient NCBI Taxonomy Toolkit

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

dna2vec: Consistent vector representations of variable-length k-mers

Numerical simulations using flexible Lattice Boltzmann solvers

Activities and exercises for the Part IA computing course in Michaelmas Term

A collection of scripts and notes related to genomics and bioinformatics

SquiggleKit: A toolkit for manipulating nanopore signal data

A cool place to store your Hi-C

Inference of ploidy and heterozygosity structure using whole genome sequencing data

A tool to circularize genome assemblies

plotting and creation of masks of spatial regions

Bio4j abstract model and general entry point to the project

✏️ A versatile DNA sequence optimizer

Code examples of fast and simple k-mer counters for tutorial purposes

GCP Essentials for Bioinformatics Researchers

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

FastQC port to Qt5: A quality control tool for high throughput sequence data.

Powerful, efficient particle trajectory analysis in scientific Python.

A Python toolbox for quantitative, reproducible flow cytometry analysis

Python module for average nucleotide identity analyses

Genomics Extension for SQLite

ECG classification programs based on ML/DL methods

MOLGENIS - for scientific data: management, exploration, integration and analysis.

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

A curated list of awesome Bioinformatics libraries and software.

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

Post-analysis of immune repertoire sequencing data

SortMeRNA: next-generation sequence filtering and alignment tool

Bioinformatics Workbook repository

Scientific Python package for tight-binding calculations in solid state physics

JIGSAW is a Delaunay-based unstructured mesh generator for two- and three-dimensional geometries.

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Conda recipes for the bioconda channel.

NGLess: NGS with less work

GDL - GNU Data Language

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

Single cell perturbation prediction

APBS - software for biomolecular electrostatics and solvation

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)