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Hi, I’m Jared 👋

I’m a Senior Bioinformatics Research Scientist in Suzanne Baker’s lab in the Department of Developmental Neurobiology at St. Jude Children’s Research Hospital. We study oncohistone mutations in the context of pediatric high grade gliomas.

Other than analysis, I build useful tools and utilities for the lab and community. Recently, I created a basic utility called STRprofiler for comparing STR profiles between large collections and identifying potential sample swaps. This is particularly useful for labs that generate many cell lines/models, as we do.

Lately, I’ve been working on an R package called CRISPRball, which is largely based around a Shiny app of the same name for exploring, visualizing, and comparing CRISPR-Cas9 screens analyzed with MAGeCK. CRISPRball is now available from Bioconductor.

I am/have been involved in a handful of Bioconductor packages, including dittoSeq, SingleR, escape, and celldex.

Here’s some stats on my GitHub repos

Jared Andrews's Projects

asospotter icon asospotter

A simplistic Shiny app for observing mutation data.

celldex icon celldex

Collection of cell type reference datasets.

crisprball icon crisprball

An interactive exploration/visualization platform to help you lift the fog from your CRISPR analyses.

dittoseq icon dittoseq

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

dittoviz icon dittoviz

Color blindness friendly visualization of any data in a data.frame format. Like dittoSeq, but not omics-structure restricted

ezscrna icon ezscrna

Convenient, high-level functions for EZ(-er) scRNA-seq analysis

gee icon gee

A dittoSeq-based Gene Expression Explorer

genotify icon genotify

A minimal desktop app for easy and convenient gene annotation and lookup.

ibet icon ibet

interactive Bioinformatics Exploratory Tools

kenpompy icon kenpompy

A simple yet comprehensive web scraper for kenpom.com.

knowledgedump icon knowledgedump

Gotta keep the brain empty to learn more. This is my easily digestible backup.

learngenomics.dev icon learngenomics.dev

A guided, intuitive introduction to genomics for software engineers. Curated by the community.

ncaahoopr icon ncaahoopr

An R package for working with NCAA Basketball Play-by-Play Data

onelineromics icon onelineromics

One liner analyses and visualizations for bulk RNA-seq and ChIP-seq data

pipelines icon pipelines

Because backups and revision history are good things.

pytfmpval icon pytfmpval

Python bindings for the TFM-Pvalue program.

rosewater icon rosewater

Expression-aware gene assignment to ROSE output

rustbucket icon rustbucket

Dumping ground for rust-backed R functions that I want to zoom.

shinyforresearchersworkshop icon shinyforresearchersworkshop

A no-nonsense introduction to Shiny for researchers, clinicians, statisticians, and scientists of all varieties, with a focus on interactive reports and re-usability.

singler icon singler

Clone of the Bioconductor repository for the SingleR package.

strprofiler icon strprofiler

A python package, command-line tool, and Shiny application to compare short tandem repeat (STR) profiles.

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