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