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/perturbation_benchmarking
Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.
ekernf01/ggrn
Python implementation for a flexible Grammar of Gene Regulatory Network inference methods (GGRN)
ekernf01/pereggrn
Infrastructure for benchmarking tools that predict perturbation responses.
ekernf01/knockoffs_paper
Landing page for our knockoff TRN project
ekernf01/perturbation_data
A collection of transcriptomic data on genetic perturbations.
ekernf01/geneformer_embeddings
A wrapper to extract perturbed cell embeddings from GeneFormer.
ekernf01/network_collection
A collection of gene regulatory networks, mostly but not entirely from chromatin data & ChIP or motif analysis.
ekernf01/rlookc
Leave-one-out knockoffs for efficient structure learning in R
ekernf01/battle-lab-guide
Battle Lab guide to MARCC
ekernf01/BINCO
A fork and update of BINCO, previously found at https://cran.r-project.org/package=BINCO
ekernf01/dcdfg
ekernf01/ekernf01.github.io
Build a Jekyll blog in minutes, without touching the command line.
ekernf01/ggrn_backend2
Wrapper allowing use of DCD-FG with a standardized interface
ekernf01/ggrn_backend3
Flexible software for declarative specification of inference methods for gene regulatory networks
ekernf01/ggrn_docker_backend
Tutorial describing how to make an arbitrary backend for GGRN via Docker.
ekernf01/GM
Gaussian Mirror R Package
ekernf01/HEART_choosing_stat_methods
A short freshman course on criteria for choosing statistical methods.
ekernf01/jlookc
Julia code for loading and using compact leave-one-out knockoffs.
ekernf01/knockoffs_BEELINE
Adaptation of the BEELINE single-cell GRN benchmarking framework.
ekernf01/knockoffs_boolode
Data generation for our "easy mode" benchmarking of model-X knockoffs.
ekernf01/knockoffs_ecoli
E. coli experiments for our manuscript "General conditional hypothesis tests suggest fundamental limits on regulatory network identification".
ekernf01/knockoffs_quick_demo
A quick demonstration of the most important distinctive features of rlookc.
ekernf01/knockoffs_shareseq
Experiments on mammalian multi-omics data for our manuscript on knockoffs and TRN inference.
ekernf01/oneSC
infer transcription factors circuits, simulate single cell expression trajectories
ekernf01/pereggrn_networks
Companion package for our collection of gene regulatory networks
ekernf01/pereggrn_perturbations
Loader package accompanying our collection of perturbation data.
ekernf01/prescient
Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
ekernf01/pylookc
Python code for loading and using compact leave-one-out knockoffs.
ekernf01/reformatVoterList
For internal use during the April 2024 TRU-UE contract ratification vote.
ekernf01/RNAForecaster.jl
Original RNAForecaster