Pinned Repositories
BioBombe
BioBombe: Sequentially compressed gene expression features enhances biological signatures
continuous_analysis
Computational reproducibility using Continuous Integration to produce verifiable end-to-end runs of scientific analysis.
covid19-review
A collaborative review of the emerging COVID-19 literature. Join the chat here:
crossref
Download metadata for all DOIs using the Crossref API
deep-review
A collaboratively written review paper on deep learning, genomics, and precision medicine
lab-website-template
An easy-to-use, flexible website template for labs.
pancancer
Building classifiers using cancer transcriptomes across 33 different cancer-types
scihub
Source code and data analyses for the Sci-Hub Coverage Study
SPRINT_gan
Privacy-preserving generative deep neural networks support clinical data sharing
tybalt
Training and evaluating a variational autoencoder for pan-cancer gene expression data
Greene Laboratory's Repositories
greenelab/lab-website-template
An easy-to-use, flexible website template for labs.
greenelab/BioBombe
BioBombe: Sequentially compressed gene expression features enhances biological signatures
greenelab/onboarding
Onboarding materials for the Greene Lab
greenelab/ccc
greenelab/hclust
Agglomerative hierarchical clustering in JavaScript
greenelab/manubot-gpt-manuscript
Manuscript describing software for the automated revision of manubot manuscripts.
greenelab/phenoplier
PhenoPLIER
greenelab/scrumlord
Continuous administration of the Greene Lab's electronic scrum
greenelab/pancancer-evaluation
Evaluating genome-wide prediction of driver mutations using pan-cancer data
greenelab/word-lapse
Explore how a word changes over time
greenelab/nature_news_disparities
Analysis pipeline for Nature news articles
greenelab/buddi
BuDDI model implementation
greenelab/xswap-manuscript
Manuscript on XSwap network permutation and hetnet node degrees
greenelab/adage-backend
The backend for Adage web app
greenelab/buddi_analysis
Analysis notebooks for the BuDDI manuscript
greenelab/lab-website-template-docs
GitBook documentation for Lab Website Template
greenelab/pred_missing_celltypes
Predicting missing cell-type proportions from deconvolution residual using NNLS.
greenelab/ccc-manuscript
greenelab/greenelab.com
The website source code for greenelab.com
greenelab/phenoplier_manuscript
PhenoPLIER manuscript
greenelab/generalization-manuscript
greenelab/hgsc_rnaseq_cluster
greenelab/aml_cfdna_atac
Using BuDDI to integrate cfDNA and ATAC data from AML samples to identify cell of origin
greenelab/backup
Backup a GitHub user's or organization's repos and wikis
greenelab/buddi_atac
greenelab/CNN_deconvolution
Ongoing project on deconvolution using higher-dimensional image representations of gene expression data.
greenelab/deconvolution_adipocytes
The following repository is a work in progress. the Aim is to deconvolve HGSOC samples with added adipocyte signal.
greenelab/deconvolution_sc_sn_comparison
The following repository is a work in progress. The Aim is to deconvolve samples with SC and SN, comparing performance.
greenelab/nature_news_manuscript
greenelab/single_translator_VAE
Implementation of a VAE in scvi-tools for single-cell and single-nucleus translation.