Python Biological-sequences Resources

Sc2rf - SARS-Cov-2 Recombinant Finder Pronounced: Scarf What's this? Sc2rf can search genome sequences of SARS-CoV-2 for potential recombinants - new

pytorch-lifestream a library built upon PyTorch for building embeddings on discrete event sequences using self-supervision. It can process terabyte-si

CodeFill This repository contains the code for our paper titled as "CodeFill: Multi-token Code Completion by Jointly Learning from Structure and Namin

ParsBigBird: Persian Bert For Long-Range Sequences The Bert and ParsBert algorithms can handle texts with token lengths of up to 512, however, many ta

Description: ProtFeat is designed to extract the protein features by employing POSSUM and iFeature python-based tools. ProtFeat includes a total of 39

Tuple Sum Filter A library to play with filtering numeric sequences by sums of t

Neighbor2Seq: Deep Learning on Massive Graphs by Transforming Neighbors to Sequences This repository is an official PyTorch implementation of Neighbor

Doughskript interpreter for converting simple command sequences into executable Arduino C++ code.

Adversarially-Robust-Periphery Code + Data from the paper "Finding Biological Plausibility for Adversarially Robust Features via Metameric Tasks" by A

Contrastive Instance Association for 4D Panoptic Segmentation using Sequences of 3D LiDAR Scans This repository contains the implementation of the pap

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

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

codon_optimize_cds_with_many_taxids_singlefasta Linux GUI app to codon optimize many single-fasta files with coding sequences, using many taxonomy ids

'rl_UK' is an open-source command-line tool in Python for calculating the shortest path between BUS stop sequences in the UK. As input files, it uses an ATCO-CIF file and 'OS Open Roads' dataset from Ordnance Survey Data Hub.

music-ai Deep learning transformer model that generates unique music sequences. Abstract In 2017, a new state-of-the-art was published for natural lan

Memory Compressed Attention Implementation of the Self-Attention layer of the proposed Memory-Compressed Attention, in Pytorch. This repository offers

ContinualPassageRanking Repository for the paper "Continual Learning of Long Topic Sequences in Neural Information Retrieval". In this repository you

MothPruning Scientific Overview Originally inspired by biological nervous systems, deep neural networks (DNNs) are powerful computational tools for mo

SCROLLS This repository contains the official code of the paper: "SCROLLS: Standardized CompaRison Over Long Language Sequences". Links Official Websi

LSTM Neural Network for Time Series Prediction LSTM built using the Keras Python package to predict time series steps and sequences. Includes sine wav

Generating Smooth Pose Sequences for Diverse Human Motion Prediction This is official implementation for the paper Generating Smooth Pose Sequences fo

(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

BioThings SDK Quick Summary BioThings SDK provides a Python-based toolkit to build high-performance data APIs (or web services) from a single data sou

jBrain Software associated with the AAAI 2022 paper Francesco D'Amore, Daniel Mitropolsky, Pierluigi Crescenzi, Emanuele Natale, Christos H. Papadimit

Annotating "hypothetical" proteins with the PDB See config/ for configuration information. This workflow takes as input a set of protein sequences. It

SeqLike - flexible biological sequence objects in Python Introduction A single object API that makes working with biological sequences in Python more

Status: Archive (code is provided as-is, no updates expected) Update August 2020: For an example repository that achieves state-of-the-art modeling pe

Self-Supervised Learning (SimCLR) with Biological Plausible Image Augmentations Official code base for the poster "On the use of Cortical Magnificatio

GebPy is a Python-based, open source tool for the generation of geological data of minerals, rocks and complete lithological sequences. The data can be generated randomly or with respect to user-defined constraints, for example a specific element concentration within minerals and rocks or the order of units within a complete lithological profile.

ObjSequenceViewer V0.5 A minimal, standalone viewer for 3D animations stored as stop-motion sequences of individual .obj mesh files. Installation: pip

Knowledge Graph Embeddings and Chemical Effect Prediction, 2020. Scripts and outputs related to the paper Prediction of Adverse Biological Effects of

Codes for TIM2021 paper "Anchor-Based Spatio-Temporal Attention 3-D Convolutional Networks for Dynamic 3-D Point Cloud Sequences"

Garment4D [PDF] | [OpenReview] | [Project Page] Overview This is the codebase for our NeurIPS 2021 paper Garment4D: Garment Reconstruction from Point

AimCLR This is an official PyTorch implementation of "Contrastive Learning from Extremely Augmented Skeleton Sequences for Self-supervised Action Reco

Garment4D [PDF] | [OpenReview] | [Project Page] Overview This is the codebase for our NeurIPS 2021 paper Garment4D: Garment Reconstruction from Point

COCO-LM This repository contains the scripts for fine-tuning COCO-LM pretrained models on GLUE and SQuAD 2.0 benchmarks. Paper: COCO-LM: Correcting an

PyCellID (building...) Functions to analyze Cell-ID single-cell cytometry data using python language. Dependecies for this project. attrs(=21.1.0) fo

AimCLR This is an official PyTorch implementation of "Contrastive Learning from Extremely Augmented Skeleton Sequences for Self-supervised Action Reco

DeepGeneAnnotator: A tool to annotate the gene in the genome The master thesis of the "Using deep learning to predict gene structures of the coding ge

BEAR Overview This repository contains code associated with the preprint A generative nonparametric Bayesian model for whole genomes (2021), which pro

Tools to create pixel-wise object masks, bounding box labels (2D and 3D) and 3D object model (PLY triangle mesh) for object sequences filmed with an RGB-D camera. This project prepares training and testing data for various deep learning projects such as 6D object pose estimation projects singleshotpose, as well as object detection and instance segmentation projects.

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

PRIP PRIP：A Protein-RNA Interface Predictor Based on Semantics of Sequences installation gensim==3.8.3 matplotlib==3.1.3 xgboost==1.3.3 prettytable==2

ARAE Tensorflow Code Code for the paper Adversarially Regularized Autoencoders for Generating Discrete Structures by Zhao, Kim, Zhang, Rush and LeCun

Introduction MASS allows you to search a time series for a subquery resulting in an array of distances. These array of distances enable you to identif

Import Subtitles for Blender VSE Addon for adding subtitle files to blender VSE as Text sequences. Using pysub2 python module. Supported formats by py

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.

DiffuseAnimals: Reaction-Diffusion Models for the Generation of Biological Patterns Introduction Reaction-diffusion equations can be utilized in order

What is autoRICEWQ? This project aims to be a handler for input creation and running of multiple RICEWQ simulations. What is RICEWQ? From the descript

To use dowload and extract "video makes.zip" Python has to be installed https://www.python.org/ (may not work on version lower than 3.9) Has to be run

Enformer - Pytorch (wip) Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch. The original tensorflow

peptides.py Physicochemical properties and indices for amino-acid sequences. 🗺️ Overview peptides.py is a pure-Python package to compute common descr

peptides.py Physicochemical properties and indices for amino-acid sequences. 🗺️ Overview peptides.py is a pure-Python package to compute common descr

Fuzzy string matching like a boss. It uses Levenshtein Distance to calculate the differences between sequences in a simple-to-use package.

Beyond Paragraphs: NLP for Long Sequences

RealTime Sign Language Detection using Action Recognition Approach Real-Time Sign Language is commonly predicted using models whose architecture consi

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

Sampling Euler tours for uniform stimulus history Table of Contents About Examples Experiment 1 Experiment 2 Experiment 3 Experiment 4 Experiment 5 Co

Selene is a Python library and command line interface for training deep neural networks from biological sequence data such as genomes.

GANs for Biological Image Synthesis This codes implements the ICCV-2017 paper "GANs for Biological Image Synthesis". The paper and its supplementary m

A simple yet powerful TUI framework for your Python (3.7+) applications

Model-free Vehicle Tracking and State Estimation in Point Cloud Sequences 1. Introduction This project is for paper Model-free Vehicle Tracking and St

ProteinBERT - Pytorch (wip) Implementation of ProteinBERT in Pytorch. Original Repository Install $ pip install protein-bert-pytorch Usage import torc

OEIS explorer This is a tool for exploring two different kinds of relationships between sequences in the OEIS: mentions (links) of other sequences on

ProteinBERT - Pytorch (wip) Implementation of ProteinBERT in Pytorch. Original Repository Install $ pip install protein-bert-pytorch Usage import torc

M4Depth This is the reference TensorFlow implementation for training and testing depth estimation models using the method described in M4Depth: A moti

CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

PSTNet: Point Spatio-Temporal Convolution on Point Cloud Sequences Introduction Point cloud sequences are irregular and unordered in the spatial dimen

COCO LM Pretraining (wip) Implementation of COCO-LM, Correcting and Contrasting Text Sequences for Language Model Pretraining, in Pytorch. They were a

CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure

TextDistance TextDistance -- python library for comparing distance between two or more sequences by many algorithms. Features: 30+ algorithms Pure pyt

TextDistance TextDistance -- python library for comparing distance between two or more sequences by many algorithms. Features: 30+ algorithms Pure pyt

BigBird, is a sparse-attention based transformer which extends Transformer based models, such as BERT to much longer sequences. Moreover, BigBird comes along with a theoretical understanding of the capabilities of a complete transformer that the sparse model can handle.

TextDistance TextDistance -- python library for comparing distance between two or more sequences by many algorithms. Features: 30+ algorithms Pure pyt

Yase Yet Another Sequence Encoder - encode sequences to vector of vectors in python ! Why Yase ? Yase enable you to encode any sequence which can be r