Python Structural-bioinformatics Resources

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

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

Molecular Nodes 🧬 🔬 💻 Buy Me a Coffee to Keep Development Going! Join a Community of Blender SciVis People! What is Molecular Nodes? Molecular Node

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

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

This repository contains the code for TABS, a 3D CNN-Transformer hybrid automated brain tissue segmentation algorithm using T1w structural MRI scans. TABS relies on a Res-Unet backbone, with a Vision Transformer embedded between the encoder and decoder layers.

package tests docs license stats support This repository contains FEDOT - an open-source framework for automated modeling and machine learning (AutoML

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

VolumeGAN - 3D-aware Image Synthesis via Learning Structural and Textural Representations 3D-aware Image Synthesis via Learning Structural and Textura

A collection of graph classification methods, covering embedding, deep learning, graph kernel and factorization papers

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

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)

(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

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

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

VolumeGAN - 3D-aware Image Synthesis via Learning Structural and Textural Representations 3D-aware Image Synthesis via Learning Structural and Textura

script-SV-genotyping These are the scripts used for the project of ‘Assembly of a pan-genome for global cattle reveals missing sequence and novel stru

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.

An easy to use elastic 3D structural engineering finite element analysis library for Python.

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

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

CCasGNN A new framework, collaborative cascade prediction based on graph neural networks (CCasGNN) to jointly utilize the structural characteristics,

slientruss3d : Python for stable truss analysis tool Desciption slientruss3d is a python package which can solve the resistances, internal forces and

Structural Guidance for Transformer Language Models This repository accompanies the paper, Structural Guidance for Transformer Language Models, publis

structural-probes Codebase for testing whether hidden states of neural networks encode discrete structures. Based on the paper A Structural Probe for

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

LexPOS_ko Generating Korean Slogans with phonetic and structural repetition Generating Slogans with Linguistic Features LexPOS is a sequence-to-sequen

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

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

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

counterfactual-tpp This is a repository containing code and real data for the paper Counterfactual Temporal Point Processes. Pre-requisites This code

===================================== README: Inpainting based PatchMatch ===================================== @Author: Younesse ANDAM @Conta

counterfactual-tpp This is a repository containing code and real data for the paper Counterfactual Temporal Point Processes. Pre-requisites This code

Python Causal Impact Causal inference using Bayesian structural time-series models. This package aims at defining a python equivalent of the R CausalI

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

3DFEM Python 3D finite element code This python code allows for solving 3D structural problems using the finite element method. New features will be a

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)

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

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

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

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

Structural Constraints on Information Content in Human Brain States Code accompanying the paper "The information content of brain states is explained

xtbreak estimating and testing for many known and unknown structural breaks in time series and panel data. For an overview of xtbreak test see xtbreak

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

Role-based network embedding via structural features reconstruction with degree-regularized constraint Train python main.py --dataset brazil-flights

Graph Neural Networks with Learnable Structural and Positional Representations Source code for the paper "Graph Neural Networks with Learnable Structu

PurNet Project for the TIP 2021 Paper "Salient Object Detection with Purificatory Mechanism and Structural Similarity Loss" Abstract Image-based salie

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

A geometric deep learning pipeline for predicting protein interface contacts.

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

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

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

MangaLineExtraction_PyTorch The (Official) PyTorch Implementation of the paper "Deep Extraction of Manga Structural Lines" Usage model_torch.py [sourc

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

StructDepth PyTorch implementation of our ICCV2021 paper: StructDepth: Leveraging the structural regularities for self-supervised indoor depth estimat

DIML Created by Wenliang Zhao*, Yongming Rao*, Ziyi Wang, Jiwen Lu, Jie Zhou This repository contains PyTorch implementation for paper Towards Interpr

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

-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

Attention Walk ⠀⠀ A PyTorch Implementation of Watch Your Step: Learning Node Embeddings via Graph Attention (NIPS 2018). Abstract Graph embedding meth

GAM ⠀⠀ A PyTorch implementation of Graph Classification Using Structural Attention (KDD 2018). Abstract Graph classification is a problem with practic

Visual-Reasoning-eXplanation [CVPR 2021 A Peek Into the Reasoning of Neural Networks: Interpreting with Structural Visual Concepts] Project Page | Vid

This repository contains FEDOT - an open-source framework for automated modeling and machine learning (AutoML). It can build custom modeling pipelines for different real-world processes in an automated way using an evolutionary approach. FEDOT supports classification (binary and multiclass), regression, clustering, and time series prediction tasks.

SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge Graph Summarization This is the code for our paper ``SumGNN: Multi-typed Drug

Collection of useful code related to biological analysis. Much of this is discussed with examples at Blue collar bioinformatics. All code, images and

Learning Structural Edits via Incremental Tree Transformations Code for "Learning Structural Edits via Incremental Tree Transformations" (ICLR'21) 1.

SARS-CoV-2 processing requests Request execution of Galaxy SARS-CoV-2 variation analysis workflows on input data you provide. Prerequisites This autom

Structural basis for solubility in protein expression systems Large-scale protein production for biotechnology and biopharmaceutical applications rely

Commonsense Knowledge Base Completion with Structural and Semantic Context Code for the paper Commonsense Knowledge Base Completion with Structural an

SLM: Structural Language Models of Code This is an official implementation of the model described in: "Structural Language Models of Code" [PDF] To ap

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

This repository contains custom pipes and models related to using spaCy for scientific documents. In particular, there is a custom tokenizer that adds

Dash Dash is the most downloaded, trusted Python framework for building ML & data science web apps. Built on top of Plotly.js, React and Flask, Dash t

Awesome Pattern Matching (apm) for Python pip install awesome-pattern-matching Simple Powerful Extensible Composable Functional Python 3.7+, PyPy3.7+

This repository contains custom pipes and models related to using spaCy for scientific documents. In particular, there is a custom tokenizer that adds

Dash Dash is the most downloaded, trusted Python framework for building ML & data science web apps. Built on top of Plotly.js, React and Flask, Dash t

Collection of useful code related to biological analysis. Much of this is discussed with examples at Blue collar bioinformatics. All code, images and

Dash Dash is the most downloaded, trusted Python framework for building ML & data science web apps. Built on top of Plotly.js, React and Flask, Dash t

Documentation: https://raamana.github.io/neuropredict/ News As of v0.6, neuropredict now supports regression applications i.e. predicting continuous t