Discover greenelab/connectivity-search-manuscript Open Source project

An easy-to-use, flexible website template for labs.

1,248

lab-website-template

Source code and data analyses for the Sci-Hub Coverage Study

338

scihub

Training and evaluating a variational autoencoder for pan-cancer gene expression data

291

tybalt

Building classifiers using cancer transcriptomes across 33 different cancer-types

162

pancancer

A collaborative review of the emerging COVID-19 literature. Join the chat here:

118

covid19-review

TeX

116

SPRINT_gan

Privacy-preserving generative deep neural networks support clinical data sharing

Computational reproducibility using Continuous Integration to produce verifiable end-to-end runs of scientific analysis.

104

continuous_analysis

BioBombe: Sequentially compressed gene expression features enhances biological signatures

BioBombe

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

adage

Download metadata for all DOIs using the Crossref API

crossref

Extracting biomedical relationships from literature with Snorkel 🏊

snorkeling

Manuscript describing open collaborative writing with Manubot

meta-review

An unsupervised transfer learning approach for rare disease transcriptomics

multi-plier

Retrieve and process PubTator annotations

pubtator

Denoising Autoencoders for Phenotype Stratification

DAPS

R package for normalizing RNA-seq data to make them comparable to microarray data.

TDM

RNAseq_titration_results

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

Manuscript for the Sci-Hub Coverage Study

scihub-manuscript

Onboarding materials for the Greene Lab

onboarding

shared-latent-space

Shared Latent Space VAE's

Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models

pdx_exomeseq

Materials for GCB535 at Penn.

GCB535

ccc

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

preprint-similarity-search

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

miQC

hclust

Agglomerative hierarchical clustering in JavaScript

Processing OpenCitations Data

opencitations

Manuscript describing software for the automated revision of manubot manuscripts.

manubot-gpt-manuscript

TeX

gbm_immune_validation

Validating glioblastoma immune cell immunohistochemsitry using computational deconvolution of TCGA tumors

scrumlord

Continuous administration of the Greene Lab's electronic scrum

Ten quick tips to finish that manuscript that's 90% complete.

finish-that-manuscript

phenoplier

PhenoPLIER

Distinguishing between generic and experiment-specific gene expression signals.

generic-expression-patterns

Using Machine Learning to Identify Glioblastoma patients with NF1 inactivation

nf1_inactivation

Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs

tad_pathways_pipeline

Two or three subtypes of high grade serous ovarian cancer subtypes fit data from different populations better than four

hgsc_subtypes

knowledge-graph-review

A literature review for constructing and using knowledge graphs in a biomedical setting.

hetnet connectivity search research notebooks (previously hetmech)

connectivity-search-analyses

Supplement to the report in https://greenelab.github.io/czi-hca-report/

CZI-Latent-Assessment

pancancer-evaluation

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

Curated summary of efforts to promote equity, diversity, and inclusion in computational biology PhD programs and societies.

compbio-edi

TDMresults

Scripts and data for re-creating TDM results.

gcb535challenge

We play a prediction game in our GCB 535 class. The class aims to teach students, primarily biologists, about machine learning methods and their use. This repository hosts the challenge for individuals outside of our lab.

Data for the Sci-Hub Stats Browser

scihub-browser-data

Biological ontologies as hetnets in Neo4j

hetontology

Shell

mpmp

Multimodal Pan-cancer Mutation Prediction

Overrepresentation analysis for KEGG and PID pathways using community detection

GEA_Community_Detection

Analyzing diversity of ISCB keynote speakers & fellows compared to the field of bioinformatics

iscb-diversity

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.

PathCORE-T-analysis

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

ADAGEpath

word-lapse

Explore how a word changes over time

Django backend for hetnet connectivity search

connectivity-search-backend

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

old-adage-server

A python implementation of Stability NMF

staNMF

Application to "Collaborative Computational Tools for the Human Cell Atlas" https://chanzuckerberg.com/initiatives/rfa

czi-rfa

rheum-plier-data

Data repository for the MultiPLIER project

linear_signal

Comparing the performance of linear and nonlinear models in transcriptomic prediction

Analysis of ISCB Fellows and Keynotes Reveals Disparities

iscb-diversity-manuscript

A literature review of biologically constrained machine learning models

biopriors-review

Analysis pipeline for Nature news articles

nature_news_disparities

annotation-refinery

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

Case-control genetics datasets evolved to be epistatic

model-free-data

PostScript

simulate-expression-compendia

Evaluating the effect of technical sources of variability in large-scale gene expression compendia.

Collecting data on whether library access to scholarly literature

library-access

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

2022-microberna

Name-based nationality prediction trained on Wikipedia

wiki-nationality-estimate

This is an upgraded version of the original snorkeling project.

snorkeling-full-text

A simple phylogenetic tree building example of Continuous Analysis

continuous_analysis_phylo

Shell

greedy-geneset-selection

Source code associated with "Leveraging global gene expression patterns to predict expression of unmeasured genes"

PathCORE-T

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

Multi-class KRAS/NRAS Classifier for Multiple Myeloma

multiple-myeloma-classifier

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

adni-netwas

Annotating Rxiv preprints in an automated fashion

annorxiver

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

adage-frontend

Detecting Biomedical Relationships using Word2vec On Pubtator Central

biovectors

Manuscript is on using snorkel to extract Heterogeneous Relationships from Pubmed Abstracts.

text_mined_hetnet_manuscript

Manuscript on XSwap network permutation and hetnet node degrees

xswap-manuscript

Analysis and experiments for https://github.com/greenelab/xswap-manuscript

xswap-analysis

A repository that collects our findings from our efforts under the CZI/HCA project.

czi-hca-report

CSS

tribe

An open-source webserver that allows for easy, reproducible genomics analyses between different webservers

Training VAE on LINCS dataset.

LINCS_latent_space

Does green OA via preprinting reduce Sci-Hub usage?

greenblack

Software to distinguish between common and experiment-specific gene expression signals

sophie

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

ponyo

Example of how continuous analysis can be used for RNA-Seq differential expression.

continuous_analysis_rnaseq

django-genes

A Django package to represent genes

Frontend code for connectivity search (formerly "Hetmech")

deconvolution_pilot

connectivity-search-frontend

The backend for Adage web app

adage-backend

Transfer learning + gene expression

whistl

Rigor, Reproducibility, Transparency, and Reagent Validity for Computational Biologists

computational-reagents

Experimenting using cycleGAN to transform P. aeruginosa gene expression data between planktonic and biofilm conditions.

cycleGAN_gene_expression

Fast domain adaptation method for building prediction models on genomic data

wenda_gpu

BuDDI model implementation

buddi

linear_models_manuscript

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

2022-cf-sputum

Predicting missing cell-type proportions from deconvolution residual using NNLS.

pred_missing_celltypes

Analysis notebooks for the BuDDI manuscript

buddi_analysis

100

wenda_gpu_paper