Python Nanopore-workflow Resources

ZenBytes Join our Slack Community and become part of the ZenML family Give the main ZenML repo a GitHub star to show your love ZenBytes is a series of

A Human-in-the-Loop? workflow for creating HD images from text DALL·E Flow is an interactive workflow for generating high-definition images from text

Nanopore-Workflow Snakemake workflow to process and filter long read data from Oxford Nanopore Technologies. It is designed to compare whole human gen

Chatbot This project is about a chatbot on Telegram to study the cloud computing. You can refer to the project of chatbot-deploy which is conveinent f

Fast and customizable reconnaissance workflow tool based on simple YAML based DSL, with support of notifications and distributed workload of that work

NB Workflows Description If SQL is a lingua franca for querying data, Jupyter sh

pyrelational is a python active learning library developed by Relation Therapeutics for rapidly implementing active learning pipelines from data management, model development (and Bayesian approximation), to creating novel active learning strategies.

find_te_ins find_te_ins is designed to find Transposon Element (TE) insertions using long reads (nanopore), by alignment directly. (minimap2) Install

Trio Assembly Snakemake Workflow Input HiFi reads for child in bam format Either

Soorgeon Join our community | Newsletter | Contact us | Blog | Website | YouTube Convert monolithic Jupyter notebooks into Ploomber pipelines. soorgeo

Using DVC with PyCaret & FastAPI (Demo) This repo contains all the resources for my demo explaining how to use DVC along with other interesting tools

Alfred-Restore-Iterm-Arrangement This alfred workflow will list avaliable iTerm2

Coin Ticker for Alfred Workflow An Alfred Workflow that provides current price and status about cryptocurrency from cryptocompare.com. Supports Alfred

Exercises and project documentation for the 3. Developing your First ML Workflow of the AWS Machine Learning Engineer Nanodegree Program

Plant extraction workflow Source code for the plant extraction workflow introduced in the paper "Agricultural Plant Cataloging and Establishment of a

Alfred 4 Workflow to search through your maintained/watched/starred GitHub repositories. Setup This workflow requires a number of Python modules. Thes

Reproducible research and reusable acyclic workflows in Python. Execute code on HPC systems as if you executed them on your machine! Motivation Would

prefect-saturn prefect-saturn is a Python package that makes it easy to run Prefect Cloud flows on a Dask cluster with Saturn Cloud. For a detailed tu

Welcome to spline - the pipeline tool Important note: Since change in my job I didn't had the chance to continue on this project. My main new project

title emoji colorFrom colorTo sdk app_file pinned decontextualizer 📤 green gray streamlit main.py false Decontextualizer As a second step in improvin

Jug: A Task-Based Parallelization Framework Jug allows you to write code that is broken up into tasks and run different tasks on different processors.

Collection of useful command line utilities and snippets to help you organise your workspace and improve workflow.

VSCode-LaTeX-Inkscape A way to integrate LaTeX, VSCode, and Inkscape in macOS Abstract I use LaTeX heavily in past two years for both academic work an

YAWPS Yet Another Workflow Parser for SecurityHub "Screaming pepper" by Rum Bucolic Ape is licensed with CC BY-ND 2.0. To view a copy of this license,

signac-flow - manage workflows with signac The signac framework helps users manage and scale file-based workflows, facilitating data reuse, sharing, a

Snakemake workflow: name A Snakemake workflow for description Usage The usage of this workflow is described in the Snakemake Workflow Catalog. If

A toolkit for monitoring ONT MinION sequencing, followed by data analysis, for viral genomes amplified with tiled amplicon sequencing.

Cylc: a workflow engine for cycling systems. Repository master branch: core meta-scheduler component of cylc-8 (in development); Repository 7.8.x branch: full cylc-7 system.

Apache Airflow Apache Airflow (or simply Airflow) is a platform to programmatically author, schedule, and monitor workflows. When workflows are define

The Open-Source MLOps Orchestration Framework MLRun is an open-source MLOps framework that offers an integrative approach to managing your machine-lea

Flyte Flyte is a workflow automation platform for complex, mission-critical data, and ML processes at scale Home Page · Quick Start · Documentation ·

blender-bake-tool This is a fork of the BakeTool with some improvements that I did to have better workflow. 99.99% of work was done by BakeTool team.

pCopy This simple python script pcopy reads a list of file names and copies them to a separate folder. Pre-requisites Python 3 (ver. 3.6) How to use

PyPackage Cookiecutter This repository is a cookiecutter to quickly start a Python package. It contains a ton of very useful features 🐳 : Package man

TEMPLATES AND COMPONENTS IN ANY LANG! This is an Open Repository For Students to Contribute code in Hackoctoberfest in different Languages and Tech me

Remora Methylation/modified base calling separated from basecalling. Remora primarily provides an API to call modified bases for basecaller programs s

Automatic regional-scale earthquake catalog building workflow: EQTransformer + Siamese EQTransforme

ClearML - Auto-Magical Suite of tools to streamline your ML workflow Experiment Manager, MLOps and Data-Management ClearML Formerly known as Allegro T

DALLE tools DALLE-tools is a github repository with useful tools to categorize, annotate or check the sanity of your datasets. Installation Just clone

"Dataflow variables are spectacularly expressive in concurrent programming" Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum Quick overview Ne

PyDS CLI Helping you manage your data science projects sanely. Requirements Anaconda/Miniconda/Miniforge/Mambaforge (Mambaforge recommended!) git on y

HiFi DeepVariant + WhatsHap workflow Workflow steps align HiFi reads to reference with pbmm2 call small variants with DeepVariant, using two-pass meth

ClearML - Auto-Magical Suite of tools to streamline your ML workflow Experiment Manager, MLOps and Data-Management ClearML Formerly known as Allegro T

Hera is an Argo Workflows Python SDK. Hera aims to make workflow construction and submission easy and accessible to everyone! Hera abstracts away workflow setup details while still maintaining a consistent vocabulary with Argo Workflows.

Dagster An orchestration platform for the development, production, and observation of data assets. Dagster lets you define jobs in terms of the data f

AnimAssist Provides a quick and easy way to mod animations in FFXIV. You will need: Before anything, the VC++2012 32-bit Redist from here. Havok will

MHtyper is an end-to-end pipeline for recognized the Forensic microhaplotypes in Nanopore sequencing data. It is implemented using Python.

A pipeline that creates consensus sequences from a Nanopore reads. It clusters reads that are similar to each other and creates a consensus that is then identified using BLAST.

Obsei is a low code AI powered automation tool. It can be used in various business flows like social listening, AI based alerting, brand image analysis, comparative study and more .

Payu Payu is a climate model workflow management tool for supercomputing environments. Payu is currently only configured for use on computing clusters

SaltConf21: Adding Workflow Approval to Salt Running To run the example, install Docker and docker-compose and run the following commands: docker-comp

redun yet another redundant workflow engine redun aims to be a more expressive and efficient workflow framework, built on top of the popular Python pr

single_snake_sequencing - sc/snRNAseq Snakemake Workflow A Snakemake workflow for standardised sc/snRNAseq analysis. Every single cell analysis is sli

Presentation Remote A remote made for making presentations easier by enabling all the members to have access to change the slide and control the flow

Deep-Education This repository is now available for public use for teaching end to end workflow of deep learning. This implies that learners/researche

MONAI Deploy App SDK offers a framework and associated tools to design, develop and verify AI-driven applications in the healthcare imaging domain.

This is a simple and flexible ML workflow engine. It helps to orchestrate events across a set of microservices and create executable flow to handle requests. Engine is designed to be configurable with any microservices. Enjoy!

Stitch together Nanopore tiled amplicon data using a reference guided approach Tiled amplicon data, like those produced from primers designed with pri

Pulsemeeter A frontend to ease the use of pulseaudio's routing capabilities, mimicking voicemeeter's workflow Features Create virtual inputs and outpu

MLOps template with examples for Data pipelines, ML workflow management, API development and Monitoring.

Write maintainable, production-ready pipelines using Jupyter or your favorite text editor. Develop locally, deploy to the cloud. ☁️

Germline Mutation Calling This Snakemake workflow follows the GATK best-practice recommandations to call small germline variants. The pipeline require

A modern Python package manager with PEP 582 support.

Python library for calling Cytoscape Automation via CyREST

LOC-FLOW is an “hands-free” earthquake location workflow to process continuous seismic records: from raw waveforms to well located earthquakes with magnitude calculations. The package assembles several popular routines for sequential earthquake location refinements, suitable for catalog building ranging from local to regional scales.

A terminal UI dashboard to monitor requests for code review across Github and Gitlab repositories.

Home Install Documentation Slack Invite Cray Labs SmartSim SmartSim makes it easier to use common Machine Learning (ML) libraries like PyTorch and Ten

SmartSim makes it easier to use common Machine Learning (ML) libraries like PyTorch and TensorFlow, in High Performance Computing (HPC) simulations and workloads.

DevOps-The-Hard-Way-AWS This tutorial contains a full, real-world solution for setting up an environment that is using DevOps technologies and practic

A lightweight (serverless) native python parallel processing framework based on simple decorators and call graphs, supporting both control flow and dataflow execution paradigms as well as de-centralized CPU & GPU scheduling.

savior是一个能够进行快速集成算法模块并支持高性能部署的轻量开发框架。能够帮助将团队进行快速想法验证（PoC），避免重复的去github上找模型然后复现模型；能够帮助团队将功能进行流程拆解，很方便的提高分布式执行效率；能够有效减少代码冗余，减少不必要负担。

Viewflow Viewflow is a framework built on the top of Airflow that enables data scientists to create materialized views. It allows data scientists to f

A lightweight, GPU accelerated, SQL engine built on the RAPIDS.ai ecosystem. Get Started on app.blazingsql.com Getting Started | Documentation | Examp

Continuous Reforestation Make tree planting a part of your daily workflow. 🌳 A GitHub Action for planting trees within your development workflow usin

PICCL: Philosophical Integrator of Computational and Corpus Libraries PICCL offers a workflow for corpus building and builds on a variety of tools. Th

CRAFT: Character-Region Awareness For Text detection Packaged, Pytorch-based, easy to use, cross-platform version of the CRAFT text detector | Paper |

StackStorm is a platform for integration and automation across services and tools, taking actions in response to events. Learn more at www.stackstorm.

Apache Airflow Apache Airflow (or simply Airflow) is a platform to programmatically author, schedule, and monitor workflows. When workflows are define

Pipenv: Python Development Workflow for Humans [ ~ Dependency Scanning by PyUp.io ~ ] Pipenv is a tool that aims to bring the best of all packaging wo

git plan A better workflow for git. Git plan inverts the git workflow so that you can write your commit message first, before you start writing code.

BatchFlow BatchFlow helps you conveniently work with random or sequential batches of your data and define data processing and machine learning workflo

Reproduce, Automate, Scale your data science. Welcome to Polyaxon, a platform for building, training, and monitoring large scale deep learning applica

MOSAIC: A modular single-molecule analysis interface MOSAIC is a single molecule analysis toolbox that automatically decodes multi-state nanopore data

The latest information about Galaxy can be found on the Galaxy Community Hub. Community support is available at Galaxy Help. Galaxy Quickstart Galaxy

PyWorkflow(PyWF) - A Python Binding of C++ Workflow 概览 C++ Workflow是一个高性能的异步引擎，本项目着力于实现一个Python版的Workflow，让Python用户也能享受Workflow带来的绝佳体验。

AudioTK Audio ToolKit is a set of audio filters. It helps assembling workflows for specific audio processing workloads. The audio workflow is split in

Pipenv: Python Development Workflow for Humans [ ~ Dependency Scanning by PyUp.io ~ ] Pipenv is a tool that aims to bring the best of all packaging wo

django-viewflow Viewflow is a lightweight reusable workflow library that helps to organize people collaboration business logic in django applications.

Couler What is Couler? Couler aims to provide a unified interface for constructing and managing workflows on different workflow engines, such as Argo

Spiff Workflow Summary Spiff Workflow is a workflow engine implemented in pure Python. It is based on the excellent work of the Workflow Patterns init

Hello, world! 👋 We've rebuilt data engineering for the data science era. Prefect is a new workflow management system, designed for modern infrastruct

Luigi is a Python (3.6, 3.7 tested) package that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow managemen