Vitalii Kleshchevnikov's repositories
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 ...)
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
openproblems
Formalizing and benchmarking open problems in single-cell genomics
regNETcmap
This package provides tools to analyse CMAP data with the goal of reconstructing the regulatory network of TFs. Part of ongoing research.
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
viral_project
Identifying novel functional linear motifs in human protein interaction networks using host-viral interactions and the principle of convergent evolution