Python Cell-biology Resources

Molecular Docking integrated in Jupyter Notebooks Description | Citation | Installation | Examples | Limitations | License Table of content Descriptio

Drug Interaction Prediction with Tigerlily Documentation | Example Notebook | Youtube Video | Project Report Tigerlily is a TigerGraph based system de

GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation [OpenReview] [arXiv] [Code] The official implementation of GeoDiff: A Geome

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

scAR scAR (single cell Ambient Remover) is a package for denoising multiple single cell omics data. It can be used for multiple tasks, such as, sgRNA

Image-to-image regression with uncertainty quantification in PyTorch. Take any dataset and train a model to regress images to images with rigorous, distribution-free uncertainty quantification.

SBINN: Systems-biology informed neural network The source code for the paper M. Daneker, Z. Zhang, G. E. Karniadakis, & L. Lu. Systems biology: Identi

colab-xterm Colab-xterm allows you to open a terminal in a cell. Usage Install package and load the extension !pip install git+https://github.com/popc

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

SegPC-2021 This is the official repository for the ISBI 2021 paper Transformer Assisted Convolutional Neural Network for Cell Instance Segmentation by

cell_counting_v2 The repository includes the code for training cell counting applications. (Keras + Tensorflow) Dataset can be downloaded here : http:

BioPy is a collection (in-progress) of biologically-inspired algorithms written in Python. Some of the algorithms included are mor

Rbc-traps-generative-design - The generative design for single red clood cell hydrodynamic traps using GEFEST framework

CellRank's reproducibility repository We believe that reproducibility is key and have made it as simple as possible to reproduce our results. Please e

Sartorius - Cell Instance Segmentation https://www.kaggle.com/c/sartorius-cell-instance-segmentation Environment setup Build docker image bash .dev_sc

excel-cell-checker Description This tool checks a given .xlsx file has the struc

Single-Cell Image Analysis Package Scimap is a scalable toolkit for analyzing spatial molecular data. The underlying framework is generalizable to spa

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

pyscreener A pythonic interface to high-throughput virtual screening software Overview This repository contains the source of pyscreener, both a libra

A Parameter-free Deep Embedded Clustering Method for Single-cell RNA-seq Data Overview Clustering analysis is widely utilized in single-cell RNA-seque

Documentation | External Resources | Datasets | Examples ChemicalX is a deep learning library for drug-drug interaction, polypharmacy side effect and

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.

unitcell Python script to generate vector graphics of an oriented lattice unit cell Examples unitcell --type hexagonal --eulers 12 23 34 --axes --crys

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

Implementation of the ivis algorithm as described in the paper Structure-preserving visualisation of high dimensional single-cell datasets.

The Stem Cell Hypothesis Codes for our paper The Stem Cell Hypothesis: Dilemma behind Multi-Task Learning with Transformer Encoders published to EMNLP

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

Welcome MICOM is a Python package for metabolic modeling of microbial communities currently developed in the Gibbons Lab at the Institute for Systems

Scripts for "Current best-practices in single-cell RNA-seq: a tutorial" This repository is complementary to the publication: M.D. Luecken, F.J. Theis,

Cellpose | A generalist algorithm for cell and nucleus segmentation. Cellpose was written by Carsen Stringer and Marius Pachitariu. To learn about Cel

tree-SNE t-SNE and hierarchical clustering are popular methods of exploratory data analysis, particularly in biology. Building on recent advances in s

PhenoGraph for Python3 PhenoGraph is a clustering method designed for high-dimensional single-cell data. It works by creating a graph ("network") repr

A Python adaption of Augur to prioritize cell types in perturbation analysis.

Cellpose | A generalist algorithm for cell and nucleus segmentation. Cellpose was written by Carsen Stringer and Marius Pachitariu. To learn about Cel

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

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

Map single-cell transcriptomes to copy number evolutionary trees. Check out the tutorial for more information. Installation $ pip install scatrex SCA

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

pcnaDeep-napari A customized interface for single cell track visualisation based on pcnaDeep and napari. 👀 Under construction You can get test image

On Path Integration of Grid Cells: Group Representation and Isotropic Scaling This repo contains the official implementation for the paper On Path Int

A totally unrealistic cell growth/reproduction simulation.

Kaggle: Cell Instance Segmentation The goal of this challenge is to detect cells in microscope images. with simple view on how many cels have been ann

AMAZ3DSim AMAZ3DSim is a lightweight python-based 3D network multi-agent simulator. It uses a cell-based congestion model. It calculates risk, battery

starfish: scalable pipelines for image-based transcriptomics starfish is a Python library for processing images of image-based spatial transcriptomics

Mathematical modeling is a powerful method for the analysis of complex biological systems. Although there are many researches devoted on produ

scBALF Covid-19 dataset Analysis Here is the Github page that has the codes for the bioinformatics pipeline described in the paper COVID-Datathon: Bio

LIVECell dataset This document contains instructions of how to access the data associated with the submitted manuscript "LIVECell - A large-scale data

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

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

CW Networks This repository contains the code used for the papers Weisfeiler and Lehman Go Cellular: CW Networks (Under review) and Weisfeiler and Leh

ncem Features Repository for the manuscript Fischer, D. S., Schaar, A. C. and Theis, F. Learning cell communication from spatial graphs of cells. 2021

Scirpy: A Scanpy extension for analyzing single-cell immune-cell receptor sequencing data Scirpy is a scalable python-toolkit to analyse T cell recept

kaggle-hpa-2021-7th-place-solution Code for 7th place solution of Human Protein Atlas - Single Cell Classification on Kaggle. A description of the met

Interpretation of T cell states using reference single-cell atlases ProjecTILs is a computational method to project scRNA-seq data into reference sing

Table of contents What is PEM? Overview Installation Usage Executable Library Telegram Bot Try OPEM in Your Browser! MATLAB Issues & Bug Reports Contr

an interactive explorer for single-cell transcriptomics data cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell tra

cochlea cochlea is a collection of inner ear models. All models are easily accessible as Python functions. They take sound signal as input and return