82 Open source projects that are alternatives of or similar to cellrank

Spatial Single Cell Analysis in Python

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

TLDR is an unsupervised dimensionality reduction method that combines neighborhood embedding learning with the simplicity and effectiveness of recent self-supervised learning losses

Quadcopter Simulation and Control. Dynamics generated with PyDy.

A comprehensive dimensional reduction framework to recover the latent topology from high-dimensional data.

Statistical Machine Intelligence & Learning Engine

Manhattan plot Generator

Reference mapping for single-cell genomics

Pyro models of SARS-CoV-2 variants

Signac

Udacity Self-Driving Car Nanodegree - Path Planning Project

No description or website provided.

🦜 DISCOTRESS 🦜 is a software package to simulate and analyse the dynamics on arbitrary Markov chains

Forward-time simulation in Python using fwdpp

Master thesis: Structured Auto-Encoder with application to Music Genre Recognition (code)

Code to compute the XP-CLR statistic to infer natural selection

An interactive 3D web viewer of up to million points on one screen that represent data. Provides interaction for viewing high-dimensional data that has been previously embedded in 3D or 2D. Based on graphosaurus.js and three.js. For a Linux release of a complete embedding+visualization pipeline please visit https://github.com/sonjageorgievska/Em…

Genome-wide imputation pipeline

Tutorials, workflows, and convenience scripts for Single Cell Portal

A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data

Cloud-based single-cell copy-number variation analysis tool

Trajectory utilities for MAVs

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

A tool to plot significant regions of GWAS

Stacked Denoising AutoEncoder based on TensorFlow

Auto generate text using Markov models.

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

No description or website provided.

No description or website provided.

Applied Probability Theory for Everyone

A standalone and free application to explore genetics variations from VCF file

An example project that predicts risk of credit card default using a Logistic Regression classifier and a 30,000 sample dataset.

Genetics (Initialization, Selection, Crossover, Mutation)

A set of notebooks as a guide to the process of fine-grained image classification of birds species, using PyTorch based deep neural networks.

A Bayesian model for compositional single-cell data analysis

Tensorflow implementation of adversarial auto-encoder for MNIST

Fast API server for calculating linkage disequilibrium

Data Science and Matrix Optimization course

Binomica Public Repository for Biological Parts

Community-provided extensions to Seurat

A complete end-to-end demonstration in which we collect training data in Unity and use that data to train a deep neural network to predict the pose of a cube. This model is then deployed in a simulated robotic pick-and-place task.

A deep learning based bioinformatics project on epigenetics in Type 2 Diabetes.

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

High-Level Motion Library for Collaborative Robots

<<------ Use SnapATAC!!

Resource of human chromosome schematics & images

tGPLVM: A Nonparametric, Generative Model for Manifold Learning with scRNA-seq experimental data

Quadruped control architecture

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

This is the code behind the www.impute.me site. It contains algorithms for personal genome analysis, including imputation and polygenic risk score calculation

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

Markov Decision Processes in Python

Manuscript for functional prediction of transcriptomic “dark matter” across species

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Markov chain generator for Python and/or Swift

Rare variant test software for next generation sequencing data

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

A curated list of awesome bioinformatics software.

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

A software package for algebraic, geometric and combinatorial problems on linear spaces. By R. Hemmecke, R. Hemmecke, M. Köppe, P. Malkin, M. Walter