Daniel Dimitrov's repositories
biocypher
A unifying framework for biomedical research knowledge graphs
cell2cell
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
CellChat
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
decoupler-py
Python package to infer biological activities from omics data using a collection of methods.
dorothea
R package to access DoRothEA's regulons
mistyR
Multiview Intercellular SpaTial modeling framework
ecosystem-packages
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
MOFA2
Multi-Omics Factor Analysis
omixer-rpmR
An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles
omnipath
Python client for the OmniPath web service
OmnipathR
R client for the OmniPath web service
openproblems
Formalizing and benchmarking open problems in single-cell genomics
pypath
Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
single-cell-best-practices
This project is work in progress! https://www.sc-best-practices.org
Singlecell_course_2022
Teaching material for the single-cell course 2022
spatial_host_microbiome_sequencing
Spatial Host Microbiome sequencing (SHM-seq)
squidpy
Spatial Single Cell Analysis in Python
Tangram
Spatial alignment of single cell transcriptomic data.