VPetukhov

Follow

Viktor Petukhov VPetukhov

Follow

PhD in Biostatistics, University of Copenhagen

52 followers · 0 following

Tbilisi, Georgia
https://scholar.google.com/citations?user=rkEysdsAAAAJ
@PetukhovViktor

Achievements

Achievements

Organizations

VPetukhov/README.md

My open source projects

Computational biology

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 It was made at 2019 and is outdated now.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

Machine learning

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.

General

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.

Personal

Linux configs
RStudio configs

Pinned Loading

ggrastr ggrastr Public

Raster geoms for ggplot2

R 212 18
kharchenkolab/conos kharchenkolab/conos Public

R package for the joint analysis of multiple single-cell RNA-seq datasets

R 191 38
kharchenkolab/pagoda2 kharchenkolab/pagoda2 Public

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

JavaScript 204 47
kharchenkolab/dropEst kharchenkolab/dropEst Public

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

C++ 86 43
kharchenkolab/Baysor kharchenkolab/Baysor Public

Bayesian Segmentation of Spatial Transcriptomics Data

Julia 150 31
kharchenkolab/sccore kharchenkolab/sccore Public

Core utilities for single-cell RNA-seq

R 12 3