639 Open source projects that are alternatives of or similar to Plantcv

Data and analysis for the Splatter paper

An analysis and visualization platform for 'omics data

This library tackles the construction and efficient execution of computational chemistry workflows

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Official code repository for GATK versions 4 and up

UGENE is free open-source cross-platform bioinformatics software

A collection of scripts and notes related to genomics and bioinformatics

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

NGLess: NGS with less work

Data intensive science for everyone.

A repository for setting up a RNAseq workflow

🔬 Assemble large genomes using short reads

Java utilities for Bioinformatics

Signal-level algorithms for MinION data

Curated (meta)list of resources for Biology.

🌈Scaffold genome sequence assemblies using linked read sequencing data

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

A package for designing compact and comprehensive capture probe sets.

Experimental code for loading/saving XArray DataArrays to Geographic Rasters using rasterio

Modular and universal bioinformatics

Example client programs for Saphetor's VarSome annotation API

Real-time species-typing visualisation for nanopore data.

Open-source bioinformatics components for Dash

Papers about deep learning ordered by task, date. Current state-of-the-art papers are labelled.

Python package providing some useful tools when dealing with molecules and materials under periodic boundary conditions and uniform grids. This is a mirror of https://gitlab.com/ales.genova/pbcpy

Aim to be the bioinformatics repository with more and newer packages

Scientific measurement library for instruments, experiments, and live-plotting

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

Working with molecular structures in pandas DataFrames

Highly adaptable common interface for proteomics search and de novo engines

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Cutadapt removes adapter sequences from sequencing reads

The Chemistry Development Kit

Accurate sample inference from amplicon data with single nucleotide resolution

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

An open source platform for managing and analyzing biomedical big data

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification and a web application for managing and executing those WES services.

The uncompromising Snakemake code formatter

Ultra-fast and memory-efficient (meta-)genome assembler

curated list of awesome tools, tutorials and APIs for Copernicus Sentinel satellite data

Interactive network visualization in Python and Dash, powered by Cytoscape.js

Sample search by metadata and features

A D library for computational biology and bioinformatics

WebLogo 3: Sequence Logos redrawn

Structural variant and indel caller for mapped sequencing data

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

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

Bioinformatics one liners from Ming Tang

COBRApy is a package for constraint-based modeling of metabolic networks.

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

The Microbiome Interpretable Temporal Rule Engine

A high-performance, Pythonic language for bioinformatics

DOM Text Based Multiple Sequence Alignment Library

A simplified pipeline for ctDNA sequencing data analysis

A scikit-learn compatible library for graph kernels

Efficient pythonic random access to fasta subsequences

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs