dbdimitrov Goto Github PK

.github

bingleseq

BingleSeq - A user-friendly R package for Bulk and Single-cell RNA-Seq data analyses

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

corneto

CORNETO: A Unified Omics-Driven Framework for Network Inference

cosmos

decoupler-py

Python package to infer biological activities from omics data using a collection of methods.

dorothea

R package to access DoRothEA's regulons

ecosystem-packages

Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)

metalinks

mistyr

Multiview Intercellular SpaTial modeling framework

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.