93 Open source projects that are alternatives of or similar to Dna Seq Gatk Variant Calling

Reproducible Science: what, why, how

A collection of portable workflows, automation recipes and components for MLOps in a unified CK format. Note that this repository is outdated - please check the 2nd generation of the CK workflow automation meta-framework with portable MLOps and DevOps components here:

My nix configuration(s), using flakes. It's my laptop, it's my servers, it's my everything, in code.

Capture all information throughout your model's development in a reproducible way and tie results directly to the model code!

PyTorch Lightning + Hydra. A very user-friendly template for rapid and reproducible ML experimentation with best practices. ⚡🔥⚡

Experiments logging & visualization

ukbREST: efficient and streamlined data access for reproducible research of large biobanks

The collaboration workspace for Machine Learning

Portable automation meta-framework to manage, describe, connect and reuse any artifacts, scripts, tools and workflows on any platform with any software and hardware in a non-intrusive way and with minimal effort. Try it using this tutorial to modularize and automate ML Systems benchmarking from the Student Cluster Competition at SC'22:

Prepare reproducible R Markdown posters

Reproducibility for Humans: A lightweight tool to perform reproducible machine learning experiment.

Data Analysis Workflows & Reproducibility Learning Resources

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

🔨 Gitian Building made simpler on any Windows Debian/Ubuntu MacOS with Vagrant, lxc, and virtualbox

Deploy a BinderHub from scratch on Microsoft Azure

Coding Standards for the USC Biostats group

⛔ ARCHIVED ⛔

Unifying Variational Autoencoder (VAE) implementations in Pytorch (NeurIPS 2022)

Pythonic functions for creating and enhancing Hydra applications

My entry for ICLR 2018 Reproducibility Challenge for paper Synthesizing robust adversarial examples https://openreview.net/pdf?id=BJDH5M-AW

Code related to Neuroimaging Analysis Replication and Prediction Study

Short course on the targets R package

creating optimal conditions for reproducibility

declarative and reproducible Jupyter environments - powered by Nix

Create highly reproducible python environments

ReproZip is a tool that simplifies the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.

Accelerated deep learning R&D

Container-native task automation engine.

PLynx is a domain agnostic platform for managing reproducible experiments and data-oriented workflows.

Tool for encapsulating, running, and reproducing data science projects

Generic template to bootstrap your PyTorch project with PyTorch Lightning, Hydra, W&B, and DVC.

The Renku Project provides a platform and tools for reproducible and collaborative data analysis.

The Accelerator is a tool for fast and reproducible processing of large amounts of data.