ekernf01
PhD student at JHU BME @CahanLab and @battle-lab . Genomic data analysis and related areas. Blog: https://ekernf01.github.io
Pinned Repositories
DoubletFinder
R package for detecting doublets in single-cell RNA sequencing data
freezr
R package to help organize data analysis projects.
ggrn
Python implementation for a flexible Grammar of Gene Regulatory Network inference methods (GGRN)
knockoffs_paper
Landing page for our knockoff TRN project
MatrixLazyEval
R package for lazy matrices: keep sparse things sparse for a low memory footprint and efficient matvecs.
pereggrn
Infrastructure for benchmarking tools that predict perturbation responses.
perturbation_benchmarking
Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.
bubblegrid
Bubble grid plots for single-cell omics data
de_screen_analysis
Code to reproduce our analyses from the definitive endoderm screen, April 2019 Cell Reports
thymusatlasanalysis
Analysis for our 2018 Immunity paper (cell atlas of mouse thymus development).
ekernf01's Repositories
ekernf01/DoubletFinder
R package for detecting doublets in single-cell RNA sequencing data
ekernf01/freezr
R package to help organize data analysis projects.
ekernf01/MatrixLazyEval
R package for lazy matrices: keep sparse things sparse for a low memory footprint and efficient matvecs.
ekernf01/534_final_proj
Final assignment for statistical computing at UW.
ekernf01/534hw7
Eric's homework for Statistical Computing at UW
ekernf01/BEMC
ekernf01/big_data_hw2
Homework for CSE547 / STAT548 at UW
ekernf01/kniterati
Write your packages in R markdown and use kniterati::kniterate() right before devtools::document().
ekernf01/branchmodel
Fit a Y shape to your data.
ekernf01/epoch
gene regulatory network reconstruction from scRNA-Seq
ekernf01/eric_prelim_code
This project implements a method for stochastic modeling of biochemical systems.
ekernf01/GEARS
GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
ekernf01/homebrew-bugs
BUGS for Homebrew
ekernf01/IRENE
Reconstruct Gene Regulatory Networks from transcriptomics and epigenetics data and predict instructive factors of cellular conversions
ekernf01/knockoffzoom
A flexible tool for the multi-resolution localization of causal variants across the genome
ekernf01/prelim_tex_files
ekernf01/soundcharts
Working towards a flexible and easy toolkit for sonifying data.
ekernf01/spacewarps_sp2016
A collaboration with UW Astronomy, searching telescope images for gravitational lensing.
ekernf01/tftargets
:dart: Human transcription factor target genes.