sjessa

cytoscope

A Shiny app for visualizing and exploring single cell RNA-sequencing data

chromswitch

An R/Bioconductor package for detecting chromatin state switches

ggmin

Clean, minimalist theme for ggplot2 (+ a variant designed for Powerpoint)

resources

Resources and tools for reproducible research with R

rr

Custom, lightweight template workflow for reproducible research projects in R

cytokit

Toolkit for analyzing single cell RNA-seq data

fair-ML

An exploration of methods for fair machine learning

rosalind

solutions to the bioinformatics learning platform: http://rosalind.info/

chromswitch-analysis

Code and data to accompany the chromswitch paper, "chromswitch: A flexible method for detecting chromatin state switches" (Jessa and Kleinman, Bioinformatics, 2018)

ACTINN

expands

Expanding Ploidy and Allele Frequency on Nested Subpopulations (expands) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data.

ggnet

Network visualization with ggplot2

morin-rotation

Rotation with Morin lab.

Pando

Multiome GRN inference.

sjessa

GitHub profile README

super

An R package implementing supervised scores for cluster analysis results