greenelab Goto Github PK

microberna-manuscript

Manubot manuscript accompanying greenelab/2022-microberna

miqc

Flexible, probablistic metrics for quality control of scRNA-seq data

mito-filtering

An analysis that once lived in greenelab/sc-cancer-hgsc/analyses/differential_expression/smart_QC.Rmd has morphed into a potential preprint, so I'm moving the analyses related to that here.

model-free-data

Case-control genetics datasets evolved to be epistatic

mousiplier-frontend

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

mpmp

Multimodal Pan-cancer Mutation Prediction

mpmp-manuscript

multi-plier

An unsupervised transfer learning approach for rare disease transcriptomics

multiple-myeloma-classifier

Multi-class KRAS/NRAS Classifier for Multiple Myeloma

mutation-fn

Analysis of false negatives from mutation prediction classifiers

nature_news_disparities

Analysis pipeline for Nature news articles

nature_news_manuscript

netscape

Exploring the network/pathway regularization landscape for gene expression data

nf1_inactivation

Using Machine Learning to Identify Glioblastoma patients with NF1 inactivation

old-adage-server

DEPRECATED - the old Adage web app. Replaced by: https://github.com/greenelab/py3-adage-backend and https://github.com/greenelab/adage-frontend

onboarding

Onboarding materials for the Greene Lab

opencitations

Processing OpenCitations Data

optimizer-manuscript

pancancer

Building classifiers using cancer transcriptomes across 33 different cancer-types

pancancer-evaluation

Evaluating genome-wide prediction of driver mutations using pan-cancer data

pathcore-t

Methods to build a network of pathway co-occurrence relationships out of expression signatures extracted from transcriptomic compendia.

pathcore-t-analysis

This repository is in support of the PathCORE-T paper (https://doi.org/10.1101/147645). It contains all the code and necessary data/metadata to repeat all analyses in the paper.

pdx_exomeseq

Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models

phenoplier

PhenoPLIER

phenoplier_manuscript

PhenoPLIER manuscript

ponyo

Software to simulate compendium-wide gene expression data using a VAE.

preprint-bot

Twitter bot that tweets preprints and comments from BioRxiv and MedRxiv

preprint-similarity-search

A web app that uses machine learning to recommend the most suitable journals based on the text content of your preprint

prettier-config-greenelab

Prettier config

pseudomonas_latent_spaces

To explore the use of latent space transformations using pseudomonas transcriptomic data.