599 Open source projects that are alternatives of or similar to Cyvcf2

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

(formerly eelpond) an automated RNA-Seq workflow system

The Microbiome Interpretable Temporal Rule Engine

compacted de Bruijn graph construction in low memory

A simplified pipeline for ctDNA sequencing data analysis

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

De novo genome assembly and multisample variant calling

🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

Simulate genealogical trees and genomic sequence data using population genetic models

A Suite of Packages for Analysis of Big Genomic Data

A friendly next-generation interface for Genomic data discovery powered by InterMine

Remote protein homology detection suite.

Performant Pythonic GenomicRanges

Python package for graph neural networks in chemistry and biology

Bioconductor cheat sheet

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

JAMP - Just Another Metabarcoding Pipeline

Simple simulation of single-cell RNA sequencing data

VCF-kit: Assorted utilities for the variant call format

Genome inference from a population reference graph

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

Build and maintain multiple custom conda environments all in once place.

LAMBDA – the Local Aligner for Massive Biological DatA

an implementation of NSGA-II in java

DEPRECIATED! Please use nf-core/tools instead

convert your 23andme raw file to VCF | DEPRECATED, please see https://github.com/plantimals/2vcf

Fast large scale matrix visualization for the web.

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

Examples using Clustergrammer2 to explore high-dimensional datasets.

A library for generating an interactive SVG visualization of CWL workflows

Data and analysis for the Splatter paper

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

pymzML - an interface between Python and mzML Mass spectrometry Files

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

transparently build CWL and Galaxy XML tool definitions for any script that uses argparse

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

ECG classification programs based on ML/DL methods

Introduction to the Unix Shell for biologists

Emperor a tool for the analysis and visualization of large microbial ecology datasets

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

Yet Another Chimeric Read Detector

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

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

BioGrakn Knowledge Graph

Demonstrating best practices for bioinformatics command line tools

Toolkit for processing sequences in FASTA/Q formats

A library to build and execute typed scientific workflows

Guided synteny alignment between duplicated genomes (within specified quota constraint)

tools for working with genome variation graphs

Aggregate results from bioinformatics analyses across many samples into a single report.

Viral genomics analysis pipelines

AQUAS TF and histone ChIP-seq pipeline

A plotly.js React component from Plotly 📈

✏️ A versatile DNA sequence optimizer

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more