Python Bioinformatics-pipeline Resources

Pipeline for creating NB422-detected (ODI) catalog The repository contains a Docker-based pipeline for preprocessing observational data. The pipeline

HapDup (haplotype duplicator) is a pipeline to convert a haploid long read assembly into a dual diploid assembly. The reconstructed haplotypes

Scikit-Pipes Scikit-Learn useful pre-defined Pipelines Hub Usage: Install scikit-pipes It's advised to install sklearn-genetic using a virtual env, in

papermill is a tool for parameterizing, executing, and analyzing Jupyter Notebooks. Papermill lets you: parameterize notebooks execute notebooks This

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

Overview This is the official repo for the paper: "NÜWA: Visual Synthesis Pre-training for Neural visUal World creAtion". NÜWA is a unified multimodal

spacy-experimental: Cutting-edge experimental spaCy components and features This package includes experimental components and features for spaCy v3.x,

Crypto Stats and Tweets Data Pipeline using Airflow Introduction Project Overview This project was brought upon through Udacity's nanodegree program.

Scanpy – Single-Cell Analysis in Python Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It inc

Datashader is a data rasterization pipeline for automating the process of creating meaningful representations of large amounts of data.

kmer-collapse Collapse a set of redundant kmers to use IUPAC degenerate bases Overview Given an input set of kmers, find the smallest set of kmers tha

BookNLP BookNLP is a natural language processing pipeline that scales to books and other long documents (in English), including: Part-of-speech taggin

Predicting Yelp Review Quality Table of Contents Introduction Motivation Goal and Central Questions The Data Data Storage and ETL EDA Data Pipeline Da

Trading Tesla with Machine Learning and Sentiment Analysis An interactive program to train a Random Forest Classifier to predict Tesla daily prices us

Create postgres tables from CSV files This first section is only relate to creating tables from CSV files using postgres container alone. Just one of

This project contains the process from building a web crawler to extract the raw data of house price to create ETL pipelines using Google Could Platform services.

Automated Machine Learning Pipeline for tabular data. Designed for predictive maintenance applications, failure identification, failure prediction, condition monitoring, etc.

A simple python application for running a CI pipeline locally This app currently supports GitLab CI scripts

Two phase pipeline + Streamlit This is an example project that demonstrates how to create a pipeline that consists of two phases of execution. In betw

FEATURE ENGINEERING Business Problem: A data preprocessing and feature engineering script for a machine learning pipeline needs to be prepared. It is

Feature-Engineering Required for a machine learning pipeline data preprocessing and variable engineering script needs to be prepared. When the dataset

🏃 Simple Local CI Runner 🏃 A simple python application for running a CI pipeline locally This app currently supports GitLab CI scripts ⚙️ Setup Inst

Welcome to Official repository of deepflash2 - a deep-learning pipeline for segmentation of ambiguous microscopic images. Quick Start in 30 seconds se

Identifies the faulty wafer before it can be used for the fabrication of integrated circuits and, in photovoltaics, to manufacture solar cells. The project retrains itself after every prediction, making it more robust and generalized over time.

Created covid data pipeline using PySpark and MySQL that collected data stream from API and do some processing and store it into MYSQL database.

Bodywork deploys machine learning projects developed in Python, to Kubernetes. It helps you to: serve models as microservices execute batch jobs run r

AptaMAT Purpose AptaMat is a simple script which aims to measure differences between DNA or RNA secondary structures. The method is based on the compa

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.

Introduction orfipy is a tool written in python/cython to extract ORFs in an extremely and fast and flexible manner. Other popular ORF searching tools

AlphaFold Analyser This program produces high quality visualisations of predicted structures produced by AlphaFold. These visualisations allow the use

cLoops2: full stack analysis tool for chromatin interactions Introduction cLoops2 is an extension of our previous work, cLoops. From loop-calling base

Explore RNA-Protein interactions. RNPFind is a bioinformatics tool. It takes an RNA transcript as input and gives a list of RNA binding protein (RBP)

feta-inference Inference pipeline for our participation in the FeTA challenge 2021. Team name: TRABIT Installation Download the two folders in https:/

logdata-anomaly-miner This tool parses log data and allows to define analysis pipelines for anomaly detection. It was designed to run the analysis wit

Install vintools To download this package from pypi: pip install vintools Install the development package To download and install the developmen

Audio Quality Platform - AQP An Open Modular Python Platform for Objective Speech and Audio Quality Metrics AQP is a highly modular pipeline designed

SegmentationPipeline -- Pytorch A simple pytorch pipeline for semantic segmentation. Requirements : torch=1.9.0 tqdm albumentations=1.0.3 opencv-pyt

ToeholdTools Category Status Repository Package Build Quality A library for the analysis of toehold switch riboregulators created by the iGEM team Cit

tpcp - Tiny Pipelines for Complex Problems A generic way to build object-oriented datasets and algorithm pipelines and tools to evaluate them pip inst

Bioinformatics This is a repository of all the algorithms covered in the Bioinformatics Course part of the Cambridge Computer Science Tripos Algorithm

SNV Pipeline SNV calling pipeline developed explicitly to process individual or trio vcf files obtained from Illumina based pipeline (grch37/grch38).

biodb Common bioinformatics database construction 1.taxonomy （Substance classification database） Download the database wget -c https://ftp.ncbi.nlm.ni

ETL Pipeline for AWS Project Description In this project, ETL pipeline is build on data warehouse hosted on AWS Redshift. The data is loaded from S3 t

page_type languages products description sample python azure azure-machine-learning-service azure-devops Code which demonstrates how to set up and ope

fMRIprep Pipeline To Machine Learning(Demo) 所有配置均在config.py文件下定义 前置环境(lilab) 各个节点均安装docker，并有fmripre的镜像 可以使用conda中的base环境（相应的第三份包之后更新） 1. fmriprep scr

PdpCLI Quick Links Introduction Installation Tutorial Basic Usage Data Reader / Writer Plugins Introduction PdpCLI is a pandas DataFrame processing CL

ColossalAI An integrated large-scale model training system with efficient parallelization techniques. arXiv: Colossal-AI: A Unified Deep Learning Syst

DWIPrep: A Robust Preprocessing Pipeline for dMRI Data DWIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transp

ColossalAI An integrated large-scale model training system with efficient parallelization techniques Installation PyPI pip install colossalai Install

ycomp ycomp is a tool for working with Y-chromosome data from YFull and FTDNA. Run ycomp -h for information on how to use the program. Installation Th

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

TrackTech: Real-time tracking of subjects and objects on multiple cameras This project is part of the 2021 spring bachelor final project of the Bachel

CoVA: Context-aware Visual Attention for Webpage Information Extraction Abstract Webpage information extraction (WIE) is an important step to create k

Rce-KGQA A novel pipeline framework for multi-hop complex KGQA task. This framework mainly contains two modules, answering_filtering_module and relati

mltrace tutorial Date: October 2021 This tutorial builds a training and testing pipeline for a toy ML prediction problem: to predict whether a passeng

Accelerated DL & RL PyTorch framework for Deep Learning research and development. It was developed with a focus on reproducibility, fast experimentati

Tracking_Pipeline Tracking_Pipeline helps you to solve the tracking problem more easily I integrate detection algorithms like: Yolov5, Yolov4, YoloX,

How Long Does It Take Ordinary People To "Get Good" At Chess? TL;DR: According to 5.5 years of data from 2.3 million players and 450 million games, mo

airflow-test This is a practice on Airflow, which is Builing virtualbox env and setting Airflow on that env Installing Airflow using python virtual en

Aadhaar Number Masking Pipeline Implementation of a complete pipeline that masks the Aadhaar Number in given images to adhere to Govt. of India's Priv

hdrplus-python Open source Python implementation of the HDR+ photography pipeline, originally developped by Google and presented in a 2016 article. Th

Documentation The documentation is available on populse_mia's website here Installation From PyPI, for users By cloning the package, for developers Fr

Lale is a Python library for semi-automated data science. Lale makes it easy to automatically select algorithms and tune hyperparameters of pipelines that are compatible with scikit-learn, in a type-safe fashion.

Framework for the Complete Gaze Tracking Pipeline The figure below shows a general representation of the camera-to-screen gaze tracking pipeline [1].

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!

mlflow_hydra_optuna_the_easy_way The easy way to combine mlflow, hydra and optuna into one machine learning pipeline. Objective TODO Usage 1. build do

New to Streaming Scraper An in-progress web scraping project built with Python, R, and SQL. The scraped data are movie and TV show information. The go

Toolchest Python Client Toolchest provides APIs for scientific and bioinformatic data analysis. It allows you to abstract away the costliness of runni

MMSceneGraph Introduction MMSceneneGraph is an open source code hub for scene graph generation as well as supporting downstream tasks based on the sce

A geometric deep learning pipeline for predicting protein interface contacts.

Using AWS CDK Pipelines and AWS Lambda for multi-branch pipeline management and infrastructure deployment. This project shows how to use the AWS CDK P

pcnaDeep: a deep-learning based single-cell cycle profiler with PCNA signal Welcome! pcnaDeep integrates cutting-edge detection techniques with tracki

Este repo ilustra un proceso sencillo de automatización de transformación y modelado de datos, a través de un pipeline utilizando Luigi. Stack princip

Data lineage made simple, reliable, and automated. Effortlessly track the flow of data, understand dependencies and analyze impact. Features Visualiza

Shotgun toolkit engine for Gaffer Contact : Diego Garcia Huerta Overview Implementation of a shotgun engine for Gaffer. It supports the classic bootst

Neural Distance Embeddings for Biological Sequences Official implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTo

Cool Bioinformatics Scripts qqplot You can use this script in two ways read tons of millions of P values from stdin # python zcat pval.txt.gz | qqplo

KYC_pipline Know your customer pipeline in apache air flow For a successful pipeline run take these steps: Run you Airflow server Admin - connection

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

Multilingual Latent Dirichlet Allocation (LDA) Pipeline This project is for text clustering using the Latent Dirichlet Allocation (LDA) algorithm. It

A production-ready pipeline for text mining and subject indexing

Airflow on Docker in EC2 + GitLab's CI/CD Personal project for simple data pipeline using Airflow. Airflow will be installed inside Docker container,

Pipeline Pipeline is an asset packaging library for Django, providing both CSS and JavaScript concatenation and compression, built-in JavaScript templ

spaCyOpenTapioca A spaCy wrapper of OpenTapioca for named entity linking on Wikidata. Table of contents Installation How to use Local OpenTapioca Vizu

Pokemon Catches Data Pipeline This is a sample project to practice end-to-end data project; Terraform is used to deploy infrastructure; Kafka is the t

A Python framework for creating reproducible, maintainable and modular data science code.

WobblyStitcher Introduction A scalable implementation of WobblyStitcher Dependencies $ python -m pip install numpy scikit-image Visualization ImageJ

About This repository provides data and code for the paper: Scalable Data Annotation Pipeline for High-Quality Large Speech Datasets Development (subm

DeepConsensus DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS)

Text Classification Baseline Pipeline for fast building text classification TF-IDF + LogReg baselines. Usage Instead of writing custom code for specif

CPOST (Clara Pipeline Operator Sizing Tool) Tool to measure resource usage of Clara Platform pipeline operators Cpost is a tool that will help you run

Sample streaming Dataflow pipeline written in Python This repository contains a streaming Dataflow pipeline written in Python with Apache Beam, readin

Hello 🤟 #Team-Greider The team of 20 people for HackBio'2021 Virtual Bioinformatics Internship 💝 🖨️ 👨‍💻 HackBio: https://thehackbio.com 💬 Ask us

PHASER: A Robust and Correspondence-Free Global Pointcloud Registration Ubuntu 18.04+ROS Melodic: Overview Pointcloud registration using correspondenc

Synthetic Dataset Generator Authors: Stanislava Fedorova Alberto Tono Meher Shashwat Nigam Jiayao Zhang Amirhossein Ahmadnia Cecilia bolognesi Dominik

-Nyokong. Drug design and development team HackBio internship is a virtual bioinformatics program that introduces students and professional to advance

💻 Welcome to Team Fleming's Repo! #TeamFleming is a multicultural group of 20 young bioinformatics enthusiasts participating in the 2021 HackBio Virt

KLUE Baseline Korean(한국어) KLUE-baseline contains the baseline code for the Korean Language Understanding Evaluation (KLUE) benchmark. See our paper fo