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2018_lrp_chip

Code used for the analysis of Lrp ChIP-seq and RNA-seq data

2020_pgen_analysis

2023_mut_scan_analysis

3dunetcnn

Keras 3D U-Net Convolution Neural Network (CNN) designed for medical image segmentation

504gitexercise

Code to demonstrate simple use of github

bgtools

Simple utilities for operating on bedgraph file data

bio-anno-rs

A collection of rust utilities for reading/handling/writing file formats commonly used in bioinformatics

chipseq_pipeline

A general ChIP-seq pipeline to reproducibly process many samples at once.

cmarrt_python

Python implementation of the CMARRT algorithm for peak calling

cmdstan

CmdStan, the command line interface to Stan

codebook_organizer

For generating all possible N-bit codes for N bits, and organizing the resulting codebook to facilitate library creating in 96-well plates used in biology.

enricherator

Tools for inferring genome-wide enrichment of sequencing counts vs. input counts

hbd_enrichment_code

idr

IDR

info_theory

A collection of utilities written in rust for basic information theory

lab_meeting

Code for lab meeting 2020-04-14

mm3

Version 3 of Python mother machine analysis code

napper

Utilities and examples for screening a proteome for potential NAPs using transcriptomics data

nested_sampling

noodles

Bioinformatics I/O libraries in Rust

numpyro

Probabilistic programming with NumPy powered by JAX for autograd and JIT compilation to GPU/CPU.

onder_tnseq_analysis

Code used to produce tn-seq insertion fold-change for first submission

optimize_rs

qpcr_analysis

rstan

RStan, the R interface to Stan

stan

Stan development repository. The master branch contains the current release. The develop branch contains the latest stable development. See the Developer Process Wiki for details.