Python Dna-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

jie jie is a spatial genome aligner. This package parses true chromatin imaging signal from noise by aligning signals to a reference DNA polymer model

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.

DNA sequence classification by Deep Neural Network: Project Overview worked on the DNA sequence classification problem where the input is the DNA sequ

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

A script written in Python that returns a consensus string and profile matrix of a given DNA string(s) in FASTA format.

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

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

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

Ejemplo Algoritmo Viterbi Ejemplo de un algoritmo Viterbi aplicado a modelo ocul

Discovering local read-level DNA methylation patterns and DNA methylation heterogeneity in intermediately methylated regions

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

This program analyzes a DNA sequence and outputs snippets of DNA that are likely to be protein-coding genes.

(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

CodExt Encode/decode anything. This library extends the native codecs library (namely for adding new custom encodings and character mappings) and prov

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

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.

Transcription Factor binding predictions with Attention and Transformers A repository with exploration into using transformers to predict DNA ↔ transc

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

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

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

T-DNA Source code for the ACL-IJCNLP 2021 paper entitled Taming Pre-trained Language Models with N-gram Representations for Low-Resource Domain Adapta

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

Equi-RC Equivariant layers for RC-complement symmetry in DNA sequence data This is a repository that implements the layers as described in "Reverse-Co

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

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

A set of Python scripts to configure a freshly installed Cisco Identity Services Engine (ISE) for simple operation; in my case, a basic Cisco Software-Defined Access environment.

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

DNA Storage Simulator This monorepository contains code for a research project by Mayank Keoliya and supervised by Djordje Jevdjic, that analyzes and

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

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

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

ABOUT TOOL : DNA-RECON is an automatic web reconnaissance tool written in python. This tool made for reconnaissance and information gathering with an

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

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

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