semenko

chrome-force-pdf-inline

A Chrome extension to force PDFs to render inline (overrides Content-Disposition: attachment).

serpent-methylation-pipeline

An efficient, documented, reproducible Snakemake methylation analysis pipeline for BS-seq and EM-seq samples, including cfDNA.

aldine-powershell-computer-config

Intune-deployed Powershell configuration for Azure Active Directory-joined machines with OneDrive folder redirection.

chrome-limit-cookie-lifetime

Persistent cookies are annoying. This Chrome extension limits cookie lifetime to a user-adjustable value.

sts-risk-calculator-cli

A Python command line tool to query the Society of Thoracic Surgeons (STS) Adult Cardiac Risk Calculator API with bulk patient records.

celfie-simplified

A quick overhaul of CelFiE — cfDNA cell type of origin estimation

gordon-lab-enveloper

Mass spec partial isotopic enrichment predictions using isodist.

academicpages.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

bioconda-recipes

Conda recipes for the bioconda channel.

biscuit

BISulfite-seq CUI Toolkit

Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

cfSort

dotfiles

Refreshed personal dotfiles.

ecotyper

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

mmtest

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

pynecone-examples

A repository full of Pynecone example apps.

pyscaffold

🛠 Python project template generator with batteries included

python-template-repo

Template repository for Python projects

scvi-tools

Deep probabilistic analysis of single-cell omics data

semenko

semenko.github.io

My personal homepage.

semenkovich-lab

semenkovich.com

Static homepage for github pages.

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

t-rec-rs

Blazingly fast terminal recorder that generates animated gif images for the web written in rust

tabnet

PyTorch implementation of TabNet paper : https://arxiv.org/pdf/1908.07442.pdf

wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

xlmhg

XL-mHG: A Semiparametric Test for Enrichment in Ranked Lists.