Name: Vitalii Kleshchevnikov
Type: User
Company: Wellcome Sanger Institute
Bio: Causal & mechanistic ML/AI models of cell identity & tissue architecture, w large sc multi-omics & spatial atlases. PhD w Dr Bayraktar, Dr Teichmann, Dr Stegle.
Twitter: vitaliikl
Location: Cambridge, UK
adult_lung_mapping
Spatial mapping in the adult lung
bds-files
just keeping materials easily findable: Supplementary files for vsbuffalo book, "Bioinformatics Data Skills"
cell2location-sandbox
Testing cell2location features
cell2location_numpyro
Translation of cell2location model into numpyro (https://github.com/BayraktarLab/cell2location)
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
cell2state_tf_activation
TF activation experiments for cell2state model project
clusterprofiler
:bar_chart:added kappa score similarity to the original package: statistical analysis and visualization of functional profiles for genes and gene clusters
cortical_astrocyte_mapping
Mapping locations of cortical single astrocyte RNA-seq
darkspaceproject
Dark Space Project: how to find published but not curated interaction data
dose
:mask:Disease Ontology Semantic and Enrichment analysis
enformer-pytorch
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
fetal_gut_mapping
Spatial mapping in the fetal gut using cell2location (accompanying paper ...)
fetal_limb_mapping
Spatial mapping of human limb cell type mapping with cell2location
gene_expression_simulator
gene expression simulator: 2 sample groups, 2 gene modules, batch effect
geneprogram
Automated discovery of functional generality of gene expression
gosemsim
:golf:GO-terms Semantic Similarity Measures
imex_vs_uniprot
Characterising molecular interaction data curated into IMEx databases (IntAct)
inferelator
The official Inferelator repository maintained by current or former Bonneau lab members
labs
just keeping materials easily findable: Rmd source files for the HarvardX series PH525x
myarrayexpress
A version of ArrayExpress R package that uses data.table::fread(..., data.table = F) to read processed data
netfeaturepval
Find enriched features of neighbours in a network
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
orthologsbiomart
One-liner for mapping orthologous genes in both R and python using ENSEMBL BioMART
paretoti
R toolbox for Archetypal Analysis and Pareto Task Inference on single cell data (based on ParTI)
pitools
Protein interaction data tools, retrieving data from IntAct and most other databases
ppi_biases_workshop
Study bias in the protein network
programmingassignment2
For online courses: Repository for Programming Assignment 2 for R Programming on Coursera
protdomseq
Work with InterPro Protein Domains and FASTA Sequences (UniProt)
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
Django
The Web framework for perfectionists with deadlines.
Laravel
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft
Open source projects and samples from Microsoft.
Google
Google ❤️ Open Source for everyone.
Alibaba
Alibaba Open Source for everyone
D3
Data-Driven Documents codes.
Tencent
China tencent open source team.
