Python Bioinformatics-pipeline Resources

Optimum Transformers Accelerated NLP pipelines for fast inference 🚀 on CPU and GPU. Built with 🤗 Transformers, Optimum and ONNX runtime. Installatio

Multi-Type-TD-TSR Check it out on Source Code of our Paper: Multi-Type-TD-TSR Extracting Tables from Document Images using a Multi-stage Pipeline for

English | 简体中文 Easy Parallel Library Overview Easy Parallel Library (EPL) is a general and efficient library for distributed model training. Usability

Causality-inspired Single-source Domain Generalization for Medical Image Segmentation Arxiv preprint Repository under construction. Might still be bug

PrimeKG Website | bioRxiv Paper | Harvard Dataverse Precision Medicine Knowledge Graph (PrimeKG) presents a holistic view of diseases. PrimeKG integra

💎A high level pipeline for face landmarks detection, supports training, evaluating, exporting, inference and 100+ data augmentations, compatible with torchvision and albumentations, can easily install with pip.

Olá! Esse é o meu primeiro repo tratando de fim a fim, uma pipeline de dados abertos do governo brasileiro relacionado a compras de contrato e cronogr

MarcoPolo is a method to discover differentially expressed genes in single-cell RNA-seq data without depending on prior clustering Overview MarcoPolo

Use cases Monitor your data warehouse in minutes: Data anomalies monitoring as dbt tests Data lineage made simple, reliable, and automated dbt operati

A three-stage detection and recognition pipeline of complex meters in wild This is the first released system towards detection and recognition of comp

VAD-SLI-ASR Python scripts for a speech processing pipeline with Voice Activity

udacity-api-reporting-pipeline In this exercise, you'll use portions of each of

MOT-Tracking-by-Detection-Pipeline Tracking-by-Detection形式のMOT(Multi Object Trac

BugBane Набор утилит для аудита безопасности приложений. Основные принципы и осо

Circular genome tools (cgt) A sage package for working with circular genomes represented by signed or unsigned permutations. It includes tools for con

B4PPI Benchmarking Pipeline for the Prediction of Protein-Protein Interactions How this benchmarking pipeline has been built, and how to use it, is de

This project shows steps to build an end to end MLOps architecture that covers data prep, model training, realtime and batch inference, build model registry, track lineage of artifacts and model drift detection. It utilizes SageMaker Pipelines that offers machine learning (ML) to orchestrate SageMaker jobs and author reproducible ML pipelines.

An ETL Pipeline of a large data set from a fictitious music streaming service named Sparkify. The ETL process flows from AWS's S3 into staging tables in AWS Redshift.

Using Data Science with Machine Learning techniques (ETL pipeline and ML pipeline) to classify received messages after disasters.

[AAAI2022] Detecting Human-Object Interactions with Object-Guided Cross-Modal Calibrated Semantics Overall pipeline of OCN. Paper Link: [arXiv] [AAAI

scrapy-folder-tree This is a scrapy pipeline that provides an easy way to store files and images using various folder structures. Supported folder str

Genomics Workshop FIXME: overview of workshop Code of Conduct All participants s

Reverse engineering the dengue virus (under development 🚧 ) What is dengue? Dengue is a viral infection transmitted to humans through the bite of inf

spaCy-wrap: For Wrapping fine-tuned transformers in spaCy pipelines spaCy-wrap is minimal library intended for wrapping fine-tuned transformers from t

shap-hypetune A python package for simultaneous Hyperparameters Tuning and Features Selection for Gradient Boosting Models. Overview Hyperparameters t

Hello from magnus Magnus provides four capabilities for data teams: Compute execution plan: A DAG representation of work that you want to get done. In

E2EDNA2 - An automated pipeline for simulation of DNA aptamers complexed with small molecules and short peptides

Segmentation Training Pipeline This package is a part of Musket ML framework. Reasons to use Segmentation Pipeline Segmentation Pipeline was developed

Built a deep neural network (DNN) that functions as an end-to-end machine translation pipeline. The pipeline accepts english text as input and returns the French translation.

Ingestinator Ingestinator is my personal VFX pipeline tool for ingesting folders containing frame sequences that have been pulled and downloaded to a

Home Credit Default Risk: Open Solution This is an open solution to the Home Credit Default Risk challenge 🏡 . More competitions 🎇 Check collection

Google AI Open Images - Object Detection Track: Open Solution This is an open solution to the Google AI Open Images - Object Detection Track 😃 More c

TGS Salt Identification Challenge This is an open solution to the TGS Salt Identification Challenge. Note Unfortunately, we can no longer provide supp

Starter code: Kaggle Toxic Comment Classification Challenge More competitions 🎇 Check collection of public projects 🎁 , where you can find multiple

TweebankNLP This repo contains the new Tweebank-NER dataset and Twitter-Stanza p

Transform application Lifecycle Data and Design and ETL pipeline architecture for ingesting data from multiple sources to redshift This project is composed of two parts: Part1 and Part2

PL-LOW A high-performance deep learning model lightweight pipeline that gradually lightens deep neural networks in order to utilize high-performance d

Backup and Recovery with AWS Backup This repository provides you with a management and deployment solution for implementing Backup and Recovery with A

Sequential-GAM Pipeline code for Sequential-GAM(Genome Architecture Mapping). mapping whole_preprocess.sh include the whole processing of mapping. usa

PizzaOrders_DataPipeline There is a Tony who is owning a New Pizza shop. He knew that pizza alone was not going to help him get seed funding to expand

Christian-Iconography A computer vision pipeline to identify the "icons" in Christian paintings. A bit about iconography. Iconography is related to id

HuSpaCy: Industrial-strength Hungarian NLP HuSpaCy is a spaCy model and a library providing industrial-strength Hungarian language processing faciliti

image source EmoBERT-MLOps The goal of this repository is to build an end-to-end MLOps pipeline based on the MLOps course from Made with ML, but this

Auto Label Pipeline A practical ML pipeline for data labeling with experiment tracking using DVC Goals: Demonstrate reproducible ML Use DVC to build a

Great Expectations Always know what to expect from your data. Introduction Great Expectations helps data teams eliminate pipeline debt, through data t

BCI-ToolBox 1. Introduction BCI-ToolBox is deep learning pipeline for motor-imagery classification. This repo contains five models: ShallowConvNet, De

DevSecOps pipeline for Python Web App A Jenkins end-to-end DevSecOps pipeline for Python web application, hosted on AWS Ubuntu 20.04 Note: This projec

Cherche (search in French) allows you to create a neural search pipeline using retrievers and pre-trained language models as rankers. Cherche is meant to be used with small to medium sized corpora. Cherche's main strength is its ability to build diverse and end-to-end pipelines.

offline-training-pipeline This is the offline-training-pipeline for our project. We adopt the offline training and online prediction Machine Learning

Complete pipeline for crawling online newspaper article. The articles are stored to MongoDB. The whole pipeline is dockerized, thus the user does not need to worry about dependencies. Additionally, docker-compose is available to increase the useability for the user.

NNR and global probabilities estimation and analysis in peptides or protein fragments This module calculates global and NNR conformation dependent pro

FaceIDLight 📘 Description A lightweight face-recognition toolbox and pipeline based on tensorflow-lite with MTCNN-Face-Detection and ArcFace-Face-Rec

OCR-Pipeline-with-Keras The keras-ocr package generally consists of two parts: a Detector and a Recognizer: Detector is responsible for creating bound

A data pipeline consisting of an AWS lambda function reading data from yfinance API, an AWS Kinesis stream to receive & store data in S3 buckets and AWS Glue crawler & Athena to run SQL queries.

(简体中文|English) Quick Start | Documents | Models List PaddleSpeech is an open-source toolkit on PaddlePaddle platform for a variety of critical tasks i

data-science-on-gcp Source code accompanying book: Data Science on the Google Cloud Platform, 2nd Edition Valliappa Lakshmanan O'Reilly, Jan 2022 Bran

X-news - Pipeline data use scrapy, kafka, spark streaming, spark ML and elasticsearch, Kibana

Mini bioinformatics project: PCA on genotypes This repo contains the code from t

Lightning-Hydra-Template A clean and scalable template to kickstart your deep learning project 🚀 ⚡ 🔥 Click on Use this template to initialize new re

KOALA KOALA, the Kilofibre Optical AAT Lenslet Array, is a wide-field, high efficiency, integral field unit used by the AAOmega spectrograph on the 3.

NeoDTI NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions (Bioinformatics).

Exam assignment for Laboratory of Bioinformatics 2 (Alma Mater University of Bologna, Master in Bioinformatics)

whylogs: A Data and Machine Learning Logging Standard whylogs is an open source standard for data and ML logging whylogs logging agent is the easiest

Movies-ETL ETL pipeline on movie data using Python and postgreSQL Overview This project consisted on a automated Extraction, Transformation and Load p

(intron I nterrogator and C lassifier) intronIC is a program that can be used to classify intron sequences as minor (U12-type) or major (U2-type), usi

AYOLOv2 The main goal of this repository is to rewrite the object detection pipeline with a better code structure for better portability and adaptabil

Overview BisQue is a web-based platform specifically designed to provide researchers with organizational and quantitative analysis tools for up to 5D

pypyr task-runner cli & api for automation pipelines. Automate anything by combining commands, different scripts in different languages & applications into one pipeline process.

The DL Streamer Pipeline Zoo is a catalog of optimized media and media analytics pipelines. It includes tools for downloading pipelines and their dependencies and tools for measuring their performace.

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

Build an Amazon SageMaker Pipeline to Transform Raw Texts to A Knowledge Graph This repository provides a pipeline to create a knowledge graph from ra

qpcr-Analyser A web-based GUI for the qpcr package that allows easy, simple and high-throughput analysis of qPCR data. As is described in more detail

HiCBrowser : A simple web browser to visualize Hi-C and other genomic tracks Fidel Ramirez, José Villaveces, Vivek Bhardwaj Installation You can insta

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

Basic yet complete Machine Learning pipeline for NLP tasks This repository accompanies the article on building basic yet complete ML pipelines for sol

unipipeline simple way to build the declarative and distributed data pipelines. Why you should use it Declarative strict config Scaffolding Fully type

PyFunctional Features PyFunctional makes creating data pipelines easy by using chained functional operators. Here are a few examples of what it can do

HyperGBM Doc | 中文 We Are Hiring！ Dear folks,we are offering challenging opportunities located in Beijing for both professionals and students who are k

Welcome to Healthsea ✨ Create better access to health with spaCy. Healthsea is a pipeline for analyzing user reviews to supplement products by extract

Google Drive VFX Server VFX Pipeline About The Project Quick tutorial to setup a Google Drive Server for multiple machines access, and VFX Pipeline on

Full Spectrum Bioinformatics is a free online text designed to introduce key topics in Bioinformatics using the Python programming language. The text is written in interactive Jupyter Notebooks, which allow you to try out and modify example code and analyses.

WASP2 (Currently in pre-development): Allele-specific pipeline for unbiased read mapping(WIP), QTL discovery(WIP), and allelic-imbalance analysis Requ

How to apply? Create your config.ini file following the example provided in config.ini Choose one of the options below to run: Run with Python3 pip in

Realtime Financial Market Data Visualization and Analysis Introduction This repo shows my project about real-time stock data pipeline. All the code is

Randomised controlled trial abstract result tabulator RCT-ART is an NLP pipeline built with spaCy for converting clinical trial result sentences into

PyIOmica (pyiomica) This repository contains PyIOmica, a Python package that provides bioinformatics utilities for analyzing (dynamic) omics datasets.

Microsoft Azure provides a wide number of services for managing and storing data. One product is Microsoft Azure SQL. Which gives us the capability to create and manage instances of SQL Servers hosted in the cloud. This project, demonstrates how to use these services to manage data we collect from different sources.

Overview The sarge package provides a wrapper for subprocess which provides command pipeline functionality. This package leverages subprocess to provi

Programming in Bioinformatics - Block 3 I. Setting up Environment and Running the Code Create the environment using the pibi_block3.yml file with the

MapReader A computer vision pipeline for the semantic exploration of maps at scale MapReader is an end-to-end computer vision (CV) pipeline designed b

Zillow-Houses This repository contains full machine learning pipeline of the Zillow Houses competition on Kaggle platform. Pipeline is consists of 10

Overview dataflow-mvp provides a basic example pipeline that pulls data from an API and writes it to a BigQuery table using GCP's Dataflow (i.e., Apac

Latent Semantic Analysis Pipeline for training LSA models using Scikit-Learn. Usage Instead of writing custom code for latent semantic analysis, you j

General informations Software repository Latest release Total downloads Pypi Code health Branch Tests Coverage Links Documentation Deployment Activity

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

MapReader A computer vision pipeline for the semantic exploration of maps at scale MapReader is an end-to-end computer vision (CV) pipeline designed b

powerapps-docstring PowerApps-docstring is a console based, pipeline ready application that automatically generates user and technical documentation f

APIlocal_dbAWS_RDS Disclaimer! All data used is for educational purposes only. ETL pipeline diagram. Aim of project By creating a fully working pipe

BlenderProc2 A procedural Blender pipeline for photorealistic rendering. Documentation | Tutorials | Examples | ArXiv paper | Workshop paper Features

Sequence clustering and database creation using mmseqs, from local fasta files