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numpy-ml

Machine learning, in numpy

pacs

Probability Model of Accessible Chromatin of Single cells

personal-website

Code that'll help you kickstart a personal website that showcases your work as a software developer.

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.

pipeline

bradner lab computation pipeline scripts

plip

Pathology Language and Image Pre-Training (PLIP) is the first vision and language foundation model for Pathology AI. PLIP is a large-scale pre-trained model that can be used to extract visual and language features from pathology images and text description. The model is a fine-tuned version of the original CLIP model.

posa-14

This repository contains assignments and examples for the 2014 offering of the POSA MOOC (see www.coursera.org/course/posa for more information)

qupath

QuPath - Bioimage analysis & digital pathology

rt

Rt calculation

saige

saigegds

Scalable Implementation of Generalized mixed models using GDS files

scent

Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA

seqarray

Big Data Management of Whole-Genome Sequence Variant Calls (Development Version)

single-cell-3prime-paper

snake-ai

An AI agent that beats the classic game "Snake".

spliceai

A deep learning-based tool to identify splice variants

staar

An R package for performing STAAR procedure in whole-genome sequencing studies

staar_workflow

staarpipeline

An R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline

staarpipeline-tutorial

The tutorial for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline and STAARpipelineSummary

street-fighter-ai

This is an AI agent for Street Fighter II Champion Edition.

tadbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

text-generation-webui

A gradio web UI for running Large Language Models like LLaMA, llama.cpp, GPT-J, OPT, and GALACTICA.

training-data-analyst

Labs and demos for courses for GCP Training (http://cloud.google.com/training).

uk_biobank_gwas

Overview of the data QC, code, and GWAS summary output from the 2017 UK Biobank data release

vardoop

A parallel variant calling tool on Hadoop

vcf_to_gds_overview

Description of VCF to GDS conversion on the UK Biobank RAP

vep_plugins

Plugins for the Ensembl Variant Effect Predictor (VEP)

vt

A tool set for short variant discovery in genetic sequence data.

wgsaparsr

Code for parsing TOPMED variant annotation files produced by the WGSA annotation tool.