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deep-review
A collaboratively written review paper on deep learning, genomics, and precision medicinelab-website-template
An easy-to-use, flexible website template for labs.scihub
Source code and data analyses for the Sci-Hub Coverage Studytybalt
Training and evaluating a variational autoencoder for pan-cancer gene expression datapancancer
Building classifiers using cancer transcriptomes across 33 different cancer-typescovid19-review
A collaborative review of the emerging COVID-19 literature. Join the chat here:SPRINT_gan
Privacy-preserving generative deep neural networks support clinical data sharingcontinuous_analysis
Computational reproducibility using Continuous Integration to produce verifiable end-to-end runs of scientific analysis.BioBombe
BioBombe: Sequentially compressed gene expression features enhances biological signaturesadage
Data and code related to the paper "ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa..." Jie Tan, et al ยท mSystems ยท 2016crossref
Download metadata for all DOIs using the Crossref APIsnorkeling
Extracting biomedical relationships from literature with Snorkel ๐meta-review
Manuscript describing open collaborative writing with Manubotmulti-plier
An unsupervised transfer learning approach for rare disease transcriptomicspubtator
Retrieve and process PubTator annotationsDAPS
Denoising Autoencoders for Phenotype StratificationTDM
R package for normalizing RNA-seq data to make them comparable to microarray data.RNAseq_titration_results
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneouslyscihub-manuscript
Manuscript for the Sci-Hub Coverage Studyonboarding
Onboarding materials for the Greene Labshared-latent-space
Shared Latent Space VAE'spdx_exomeseq
Pipeline analysis for whole exome sequencing of pancreatic cancer PDX modelsGCB535
Materials for GCB535 at Penn.ccc
preprint-similarity-search
A web app that uses machine learning to recommend the most suitable journals based on the text content of your preprintmiQC
Flexible, probablistic metrics for quality control of scRNA-seq datahclust
Agglomerative hierarchical clustering in JavaScriptopencitations
Processing OpenCitations Datamanubot-gpt-manuscript
Manuscript describing software for the automated revision of manubot manuscripts.gbm_immune_validation
Validating glioblastoma immune cell immunohistochemsitry using computational deconvolution of TCGA tumorsscrumlord
Continuous administration of the Greene Lab's electronic scrumfinish-that-manuscript
Ten quick tips to finish that manuscript that's 90% complete.phenoplier
PhenoPLIERgeneric-expression-patterns
Distinguishing between generic and experiment-specific gene expression signals.nf1_inactivation
Using Machine Learning to Identify Glioblastoma patients with NF1 inactivationtad_pathways_pipeline
Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADshgsc_subtypes
Two or three subtypes of high grade serous ovarian cancer subtypes fit data from different populations better than fourknowledge-graph-review
A literature review for constructing and using knowledge graphs in a biomedical setting.connectivity-search-analyses
hetnet connectivity search research notebooks (previously hetmech)CZI-Latent-Assessment
Supplement to the report in https://greenelab.github.io/czi-hca-report/pancancer-evaluation
Evaluating genome-wide prediction of driver mutations using pan-cancer datacompbio-edi
Curated summary of efforts to promote equity, diversity, and inclusion in computational biology PhD programs and societies.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.scihub-browser-data
Data for the Sci-Hub Stats Browserhetontology
Biological ontologies as hetnets in Neo4jmpmp
Multimodal Pan-cancer Mutation PredictionGEA_Community_Detection
Overrepresentation analysis for KEGG and PID pathways using community detectioniscb-diversity
Analyzing diversity of ISCB keynote speakers & fellows compared to the field of bioinformaticsPathCORE-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.ADAGEpath
An R package (ADAGEpath) to perform signature analysis using methodology from the ADAGE manuscriptword-lapse
Explore how a word changes over timeconnectivity-search-backend
Django backend for hetnet connectivity searchold-adage-server
DEPRECATED - the old Adage web app. Replaced by: https://github.com/greenelab/py3-adage-backend and https://github.com/greenelab/adage-frontendstaNMF
A python implementation of Stability NMFczi-rfa
Application to "Collaborative Computational Tools for the Human Cell Atlas" https://chanzuckerberg.com/initiatives/rfarheum-plier-data
Data repository for the MultiPLIER projectlinear_signal
Comparing the performance of linear and nonlinear models in transcriptomic predictioniscb-diversity-manuscript
Analysis of ISCB Fellows and Keynotes Reveals Disparitiesbiopriors-review
A literature review of biologically constrained machine learning modelsnature_news_disparities
Analysis pipeline for Nature news articlesconnectivity-search-manuscript
Manuscript describing Hetnet Connectivity Searchannotation-refinery
A python package that consists of functions that process publicly available annotated sets of genesmodel-free-data
Case-control genetics datasets evolved to be epistaticsimulate-expression-compendia
Evaluating the effect of technical sources of variability in large-scale gene expression compendia.library-access
Collecting data on whether library access to scholarly literature2022-microberna
A pipeline to generate a compendia of bacterial and archaeal RNA-seq datawiki-nationality-estimate
Name-based nationality prediction trained on Wikipediasnorkeling-full-text
This is an upgraded version of the original snorkeling project.continuous_analysis_phylo
A simple phylogenetic tree building example of Continuous Analysisgreedy-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.multiple-myeloma-classifier
Multi-class KRAS/NRAS Classifier for Multiple Myelomaadni-netwas
Repository associated with Song et al. manuscript describing a Network-wide Association Study of ADNI Cohorts.annorxiver
Annotating Rxiv preprints in an automated fashionadage-frontend
The Adage web app, a tool to explore gene expression data and discover new insights from machine learning modelsbiovectors
Detecting Biomedical Relationships using Word2vec On Pubtator Centraltext_mined_hetnet_manuscript
Manuscript is on using snorkel to extract Heterogeneous Relationships from Pubmed Abstracts.xswap-manuscript
Manuscript on XSwap network permutation and hetnet node degreesxswap-analysis
Analysis and experiments for https://github.com/greenelab/xswap-manuscriptczi-hca-report
A repository that collects our findings from our efforts under the CZI/HCA project.tribe
An open-source webserver that allows for easy, reproducible genomics analyses between different webserversLINCS_latent_space
Training VAE on LINCS dataset.greenblack
Does green OA via preprinting reduce Sci-Hub usage?sophie
Software to distinguish between common and experiment-specific gene expression signalsponyo
Software to simulate compendium-wide gene expression data using a VAE.continuous_analysis_rnaseq
Example of how continuous analysis can be used for RNA-Seq differential expression.django-genes
A Django package to represent genesdeconvolution_pilot
connectivity-search-frontend
Frontend code for connectivity search (formerly "Hetmech")adage-backend
The backend for Adage web appwhistl
Transfer learning + gene expressioncomputational-reagents
Rigor, Reproducibility, Transparency, and Reagent Validity for Computational BiologistscycleGAN_gene_expression
Experimenting using cycleGAN to transform P. aeruginosa gene expression data between planktonic and biofilm conditions.wenda_gpu
Fast domain adaptation method for building prediction models on genomic databuddi
BuDDI model implementation2022-cf-sputum
Analysis of cystic fibrosis sputum RNA-seq samples for discovery of interesting gene expression pathwayspred_missing_celltypes
Predicting missing cell-type proportions from deconvolution residual using NNLS.buddi_analysis
Analysis notebooks for the BuDDI manuscriptwenda_gpu_paper
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