- dropEst: low-level pre-processing of scRNA-seq fastq files for accurate estimation of gene expression matrices (Genome Biology, 2018)
- pagoda2: processing and analysis of individual scRNA-seq samples
- conos: joint analysis of scRNA-seq collections (Nature Methods, 2019)
- cacoa: case-control analysis of scRNA-seq experiments (bioRxiv, 2022)
- Baysor: Bayesian cell segmentation in single-molecule protocols for spatially-resolved transcriptomics (Nature Biotech, 2021)
- GPTCellAnnotator: using GPT and scanpy to automatically annotate cell types in scRNA-seq data
- CellAnnotatoR: marker-based annotation of scRNA-seq data
- Comparison of single-molecule transcriptomic protocols. It was made at 2019 and is outdated now.
- vpscituls: my helper functions for single-cell analysis
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- Enforcing spatial structure on word2vec. Application of ideas from Interpretable Neuron Structuring with Graph Spectral Regularization during my participation in the AI Safety Camp
- Piecewise-linear approximation of 1D time-series using splines on stock data
- FastRandPCA.jl: Fast randomized PCA algorithms for Sparse Data, re-implementation of frPCA_sparse.
- ggrastr: rasterize individual layers for ggplot2
- dataorganizer: a research compendium package for scientific projects in R
- MailDay Extension for Thunderbird: implementation of the Maxim Dorofeev's idea on how to motivate yourself to proces old emails.
