vitkl

ParetoTI

R toolbox for Archetypal Analysis and Pareto Task Inference on single cell data (based on ParTI)

orthologsBioMART

One-liner for mapping orthologous genes in both R and python using ENSEMBL BioMART

cell2location_paper

Cell2location paper - Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics

cell2module

cell2module: decomposing scRNA and scATAC cell identity into gene modules using count-based Bayesian NMF

fetal_gut_mapping

Spatial mapping in the fetal gut using cell2location (accompanying paper ...)

PItools

Protein interaction data tools, retrieving data from IntAct and most other databases

SpaceJam

SpaceJam is an analysis platform for performing data exploration, gene DE analysis, estimating cell type abundance and prioritising cell communication events using Nanostring GeoMx data. We use probabilistic models tailored to Nanostring WTA data, extend cell2location to multiple samples and reach more detailed biological insights.

adult_lung_mapping

Spatial mapping in the adult lung

cortical_astrocyte_mapping

Mapping locations of cortical single astrocyte RNA-seq

scENTInEL

Scentinel is a probabilistic ensemble framework designed for mapping large single-cell (sc) multi-omic datasets using either transductive or inductive transfer learning. The framework operates on pre-integrated low-dimensional latent embeddings and offers multiple algorithmic modalities.

cell2state_tf_activation

TF activation experiments for cell2state model project

cell2location-sandbox

Testing cell2location features

cell2location_numpyro

Translation of cell2location model into numpyro (https://github.com/BayraktarLab/cell2location)

enformer-pytorch

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

fetal_limb_mapping

Spatial mapping of human limb cell type mapping with cell2location

numpyro

Probabilistic programming with NumPy powered by JAX for autograd and JIT compilation to GPU/TPU/CPU.

openproblems

Formalizing and benchmarking open problems in single-cell genomics

py_pcha

Python package that implements the PCHA algorithm for Archetypal Analysis by Mørup et. al.

pyro

Deep universal probabilistic programming with Python and PyTorch

random-promoter-dream-challenge-2022

regNETcmap

This package provides tools to analyse CMAP data with the goal of reconstructing the regulatory network of TFs. Part of ongoing research.

sandbox

Pyro models and misc examples.

scHPF

Single-cell Hierarchical Poisson Factorization

scvi-tools

Deep generative models for single-cell omics data

scvi-tools-skeleton

Template repository for creating novel models with scvi-tools

scvi-tutorials

Notebooks used in scvi-tools tutorials

SLIMFinderR

Tools for systematic search for short linear motifs (SLIMs) using SLIMSuite and protein interaction data in R

SPOTlight

Spatial Transcriptomics Capture Location Deconvolution

swot

Identify email addresses or domains names that belong to colleges or universities. Help automate the process of approving or rejecting academic discounts.

viral_project

Identifying novel functional linear motifs in human protein interaction networks using host-viral interactions and the principle of convergent evolution