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greenelab

98 indexed repositories · View on GitHub

deep-review
A collaboratively written review paper on deep learning, genomics, and precision medicine

HTML · 1283 stars
lab-website-template
An easy-to-use, flexible website template for labs. https://doi.org/10.5281/zenodo.17228741

HTML · 575 stars
scihub
Source code and data analyses for the Sci-Hub Coverage Study

Jupyter Notebook · 306 stars
tybalt
Training and evaluating a variational autoencoder for pan-cancer gene expression data

HTML · 176 stars
pancancer
Building classifiers using cancer transcriptomes across 33 different cancer-types

Jupyter Notebook · 127 stars
covid19-review
A collaborative review of the emerging COVID-19 literature. Join the chat here:

TeX · 119 stars
crossref
Download metadata for all DOIs using the Crossref API

Jupyter Notebook · 66 stars
BioBombe
BioBombe: Sequentially compressed gene expression features enhances biological signatures

Jupyter Notebook · 65 stars
snorkeling
Extracting biomedical relationships from literature with Snorkel 🏊

Jupyter Notebook · 58 stars
meta-review
Manuscript describing open collaborative writing with Manubot

HTML · 51 stars
multi-plier
An unsupervised transfer learning approach for rare disease transcriptomics

HTML · 49 stars
pubtator
Retrieve and process PubTator annotations

Python · 44 stars
DAPS
Denoising Autoencoders for Phenotype Stratification

HTML · 42 stars
RNAseq_titration_results
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

HTML · 37 stars
scihub-manuscript
Manuscript for the Sci-Hub Coverage Study

HTML · 34 stars
onboarding
Onboarding materials for the Greene Lab

33 stars
shared-latent-space
Shared Latent Space VAE's

Python · 29 stars
ccc

Jupyter Notebook · 26 stars
pdx_exomeseq
Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models

HTML · 23 stars
miQC
Flexible, probablistic metrics for quality control of scRNA-seq data

R · 23 stars
78 more repositories live on View on GitHub

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Query Depot: Cool Cypher queries for Hetontology Open

greenelab/hetontology#2 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Check out SciGraph Open

greenelab/hetontology#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
adding loggers Open

greenelab/staNMF#7 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
staNMF constructor should be able to take in list of K's, rather than upper/lower bound Open

greenelab/staNMF#8 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Upgrade to Python 3? Open

greenelab/staNMF#9 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Link to GEO series Open

task

greenelab/nf1_inactivation#2 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Use Microsoft R Open + Conda in Docker Build Open

greenelab/tad_pathways#16 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
add capability for custom tad regions Open

greenelab/tad_pathways#30 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Error in file(con, "w") : cannot open the connection Open

greenelab/tad_pathways#32 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
RFA Bullet Points Open

greenelab/czi-rfa#1 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
permutation test method `network_edges_permutation_test` should return both the significant edges and the final network. Open

bug

greenelab/PathCORE-T#4 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
Create a tribe-client test link on Tribe (and include the connection to it in tribe-client) for debugging when installing tribe-client on a client webserver. Open

backlog

greenelab/tribe-client#1 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Sending configuration for templates (location & filename) to app_settings, which can be overridden by server developer in settings.py file. Open

backlog

greenelab/tribe-client#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Have the client's access be able to be set as preferences by each user individually, for each client server/application. Open

backlog

greenelab/tribe-client#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Abstract code in download_files.py file to be able to interact with each service (GO, DO, KEGG) independently. Open

greenelab/annotation-refinery#1 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Abstract code that builds file paths from urls into a function, using os.path. and urlsplit Open

greenelab/annotation-refinery#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Annotation refinery creating more versions in Tribe when it looks like list of genes in the geneset is unchanged. Open

greenelab/annotation-refinery#5 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Annotation refinery is taking too long to load all of the GO, KEGG and DO sets to Tribe. Open

greenelab/annotation-refinery#6 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Move common urls among species "*.ini" files to "main_config.ini" file so that we only have to change it in one place if we need to. Open

greenelab/annotation-refinery#10 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
"download_files" not exist Open

greenelab/annotation-refinery#11 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Assign Zenodo DOI Open

greenelab/GEA_Community_Detection#26 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
What should the output of this repository be? Open

greenelab/czi-cancer-data#1 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Download Raw Data for Patel et al. 2014 Open

greenelab/czi-cancer-data#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Stats about Penn Libraries to provide readers with context Open

greenelab/library-access#23 · 10 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Run umap based on tybalt model Open

greenelab/czi-hca-report#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
List of studies that have used this data Open

greenelab/model-free-data#2 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Storing at zenodo? Open

greenelab/crossref#8 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Unicode issue - Non english characters as question mark Open

greenelab/crossref#9 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Question on keyword coverage Open

greenelab/crossref#10 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Invalid character error when using mongoimport Open

greenelab/crossref#12 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
2019-09 IA Bulk Dump Update Open

greenelab/crossref#14 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Switching from HGNC to EntrezID Open

greenelab/hgsc_subtypes#17 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Move Low Correlating Sample Exclusion to Inclusion Script Open

enhancement

greenelab/hgsc_subtypes#25 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
local estimate repo Open

help wanted

greenelab/hgsc_subtypes#28 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
k=2 clustering results Open

bug

greenelab/hgsc_subtypes#30 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Adding Module 7 Data and Results Open

greenelab/hgsc_subtypes#46 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add columns in gene and variant flow passage to indicate F0 and F5 only in TRIPLICATE sets Open

greenelab/pdx_exomeseq#48 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Variants Correlated with Chemoresistance Open

greenelab/pdx_exomeseq#52 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Compare shared mutations in 008 and 040 Open

greenelab/pdx_exomeseq#53 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
could't download docker image Open

greenelab/DAPS#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Update reference to publication Open

greenelab/DAPS#5 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
R package for classification evaluation Open

greenelab/CZI-Latent-Assessment#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Rename repository to be more general Open

greenelab/rheum-plier-data#27 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Establish naming convention for latent features Open

enhancement

greenelab/tybalt#86 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Modify Tybalt to handle missing values for incomplete data Open

stale

greenelab/tybalt#156 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Open Issues in Bitbucket Repo Open

backlog

greenelab/django-organisms#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
"BaseCommand.option_list" is deprecated Open

greenelab/django-organisms#3 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 17, 2026
Paper examples for discussion Open

greenelab/computational-reagents#4 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Continuous Analysis Open

greenelab/computational-reagents#5 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Docker Open

greenelab/computational-reagents#6 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026

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