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biokepi

Bioinformatics Ketrew Pipelines

bratreader

Python code for reading Brat Repositories. Supports saving and reading from XML files for easy acces to annotations.

caret

caret (Classification And Regression Training) R package that contains misc functions for training and plotting classification and regression models

caretensemble

caret models all the way down :turtle:

cartpipeline

Testing pipeline for CAR-T targets

cbgen-py

Python wrapper around bgen C library.

cellprofiler

An open-source application for biological image analysis

charleston-data-analytics-cancer-genomics-data-challenge

Cancer Genomics Data Challenge

charlestondatascience

Shared dumping ground for data science notebooks and things.

coclobas

Configurable Cloudy Batch Scheduler

codex

Processing worfklows for CODEX cytometric imaging data

codex-java

Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation

covid-tracking-api

COVID-19 Rest & GraphQL API for US data, using Cloudflare Workers

covidscenariopipeline

Public shared code for doing scenario forecasting and creating reports for various governmental entities.

cytometry-experiments

Shiny app for RGLab tools

dask

Parallel computing with task scheduling

dask-cloudprovider

Cloud provider cluster managers for dask distributed

dask-ml

Scalable Machine Learning with Dask

data-engineer-challenge

NBS Recruiting challenge given to prospective data engineers

data_pipeline

Code for the data processing pipeline

devtest

edward

A library for probabilistic modeling, inference, and criticism. Deep generative models, variational inference. Runs on TensorFlow.

fast-lmm

Python version of Factored Spectrally Transformed Linear Mixed Models

fcsparser

a python parser for reading fcs files supprorting fcs 2.0, 3.0, 3.1

firebrowse

Python 2/3 port of firebrowse pypi package for Broad institute TCA data

flowdec

Tensorflow Deconvolution for Microscopy

funtime-forecast

Activity ideas for kids

glow

An open-source toolkit for large-scale genomic analysis

gnomad_qc

hail

Scalable genomic data analysis.