greenelab Goto Github PK

2022-cf-sputum

Analysis of cystic fibrosis sputum RNA-seq samples for discovery of interesting gene expression pathways

2022-microberna

A pipeline to generate a compendia of bacterial and archaeal RNA-seq data

2022-refinebio-unmapped

Code to explore the unquantified fractions of refine.bio RNA-seq data sets

2022-seqadage-pa-model

Building ADAGE models using Pseudomonas aeruginosa RNA-seq data. See https://github.com/georgiadoing/seqADAGE for initial work on this application, and https://bitbucket.org/greenelab/eadage/src/master/ for original eADAGE code

2022-test-sketch-core-accessory-interactome

Determine whether some of the results genereated in greenelab/core-accessory-interactome can be regenerated using abundance-weighted FracMinHash sketches instead of gene counts

adage

Data and code related to the paper "ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa..." Jie Tan, et al · mSystems · 2016

adage-backend

The backend for Adage web app

adage-frontend

The Adage web app, a tool to explore gene expression data and discover new insights from machine learning models

adagepath

An R package (ADAGEpath) to perform signature analysis using methodology from the ADAGE manuscript

adni-netwas

Repository associated with Song et al. manuscript describing a Network-wide Association Study of ADNI Cohorts.

aml_cfdna_atac

Using BuDDI to integrate cfDNA and ATAC data from AML samples to identify cell of origin

annorxiver

Annotating Rxiv preprints in an automated fashion

annorxiver_manuscript

This manuscript covers the annorxiver project.

annotation-refinery

A python package that consists of functions that process publicly available annotated sets of genes

assets

Assets (logos, icons, animations, sounds, etc) for use in the Greene Lab

backup

Backup a GitHub user's or organization's repos and wikis

ben_heil_dissertation

biobombe

BioBombe: Sequentially compressed gene expression features enhances biological signatures

bioconductor-scraper

A scraper which tries to generate conda recipes for bioconductor and other needed R packages.

biopriors-review

A literature review of biologically constrained machine learning models

biovectors

Detecting Biomedical Relationships using Word2vec On Pubtator Central

brand

Logos and other brand assets for the Greene Lab organization

brd-net

Transfer learning for uncovering the biology underlying rare disease

buddi

BuDDI model implementation

buddi_analysis

Analysis notebooks for the BuDDI manuscript

buddi_atac

cbis_atac_2022

repository for two projects from the Colorado Biomedical Informatics Summer Fellowship Program

ccc

ccc-manuscript

ccc-manuscript-chatgpt-test-fork

Test Fork