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bcbio-nextgen

Validated, scalable, community developed variant calling and RNA-seq analysis

bcbio-nextgen-vm

Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

cbioportal

cBioPortal for Cancer Genomics

content-analyzer

cookbook

Cookbook for Node on FHIR and the clinical Meteor.js build pipeline. Create FDA, HIPPA, and HL7 compliant Javascript/Node applications!

deeppath

Classification of Lung cancer slide images using deep-learning

dnacodec

Program to encode binary files to DNA sequences with embedded error correction

docker-django-local

Dockerfiles to create images for use in local Django development environments

docker-pycron

Configurable scheduling for custom python scripts

exstra

Expanded STR algorithm for Illumina sequencing data

freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

geneimpacts

prioritize effects of variant annotations from VEP, SnpEff, et al.

how_to_build_a_bitcoin_startup

This is the code for "How to Build a Bitcoin Startup" by Siraj Raval on Youtube

igv.js

Lightweight html5 version of the Integrative Genomics Viewer

indigo

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

jscomut

An interactive co-mutation plot generator, in-browser but fully client-side. Load a data file, play with the geometry of the chart, explore your data, and save an svg file.

matplotlib-2.0-by-examples

medplum

Medplum is a healthcare platform that helps you quickly develop high-quality compliant applications.

motioncollector

iOS app for collecting data from internal motion sensors (gyroscope, magnetometer, accelerometer) of iPhone and Apple Watch.

node-on-fhir

Tech stack for building MACRA and 21st Century Cures compliant webapps.

openai-whisper-audio-transcription-and-summarization-chatbot

Web app enabling users to either record or upload audio files. Then utilizing OpenAI API (Whisper, GPT4) generates transcriptions, summaries, fact checks, sentiment analysis, and text metrics. Users can also intelligently chat about their transcriptions with a GPT4 chatbot. Data is stored relationally in SQLite and also vectorized in Pinecone.

phenotips

PhenoTips provides an easy-to-use Web interface and standardized database back-end for collecting clinical findings observed in patients with possible genetic disorders.

serverless-summarize-foundational-model

stain_adversarial_learning

Using adversarial feature learning and color augmentation to address the variability in histopathology images

staintools

Tools for tissue image stain normalization and augmentation in Python 3. [python, scientific]

streamlit_whisper_transcription

Streamlit Audio Transcription with OPENAI's Whisper Ai: An interactive Streamlit app demonstrating real-time audio transcription using OPENAI's Whisper Ai.

teal

Sanger Trace Viewer

tracy

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

varapp-backend-py

Django backend to varapp