599 Open source projects that are alternatives of or similar to Hap.py

Detection of NCLDV signatures in 'omic data

Python module for average nucleotide identity analyses

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

The uncompromising Snakemake code formatter

Protein-Level ASSembler (PLASS): sensitive and precise protein assembler

A D library for computational biology and bioinformatics

Core BioPerl 1.x code

Remote protein homology detection suite.

Fast large scale matrix visualization for the web.

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

A wrapper for the EnsEMBL REST API

Fast & accurate alignment of barcoded short-reads

ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

DOM Text Based Multiple Sequence Alignment Library

Solutions to assignments of Coursera Specializations - Deep learning, Machine learning, Algorithms & Data Structures, Image Processing and Python For Everybody

MMseqs2 app to run on your workstation or servers

Phylogenetic trees in Julia

Global Biotic Interactions provides access to existing species interaction datasets

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

(No maintenance) Detect gene fusion directly from raw fastq files

Generic germline variant annotation pipeline

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

A comprehensive library for computational molecular biology

No description or website provided.

Personal Cancer Genome Reporter (PCGR)

A Practical and Efficient NCBI Taxonomy Toolkit

(formerly eelpond) an automated RNA-Seq workflow system

Performant Pythonic GenomicRanges

A collaboratively written review paper on deep learning, genomics, and precision medicine

MISO: An open-source LIMS for NGS sequencing centres

A Suite of Packages for Analysis of Big Genomic Data

📊 Identify cell types and pathways affected by genetic risk loci.

Parser and database to index the terpene profile of different strains of Cannabis from online databases

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

Chromosome visualization for the web

A tutorial on methods of 16S analysis with QIIME 1

variant expressions, annotation, and filtering for great good.

JAMP - Just Another Metabarcoding Pipeline

Fast multi-line FASTA/Q reader in several programming languages

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

Development repository for the Bioconductor package 'mixOmics '

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

Tools for working with genomic and high throughput sequencing data.

SortMeRNA: next-generation sequence filtering and alignment tool

an implementation of NSGA-II in java

🚦 Run Picard on BAM files and collate 90 metrics into one file.

vCard Serializer and Parser for C#

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

Python Programming for Biologists

DEPRECIATED! Please use nf-core/tools instead

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.

Data and analysis for the Splatter paper

A Python package for fast operations on 1-dimensional genomic signal tracks

Simulate genealogical trees and genomic sequence data using population genetic models

A robust model for quantitative comparison of ChIP-Seq data sets.

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

Robust, flexible and resource-efficient pipelines using Go and the commandline

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms