An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.

Find profile pairs and compute retrieval metrics between them.

Single cell Morphology Quality Control (coSMicQC)

Map of Open Source Science

This Nextflow workflow main.nf performs a high-level quality check on tools.

An open-source handbook of applied guidance and tools for sustainable software development and maintenance.

Python package for processing image-based profiling data

A generative AI extension for JupyterLab

A repository for presentations from the DBMI Software Engineering Team (SET)

Fast Gene Set Enrichment Analysis (GSEA) implementation of the prerank algorithm. Use Loess interpolation of bimodal ES distribution for accurate p-value estimation.

Better Scientific Software Homepage

Code for Dharia NV, et al. A First-Generation Pediatric Cancer Dependency Map. Nature Genetics 2021.

Analysis repository understanding striation patterns in macrophages.

Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.

Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/

Benchmarking data processing strategies for Cell Painting data of NF1 Schwann cells. See analysis repository (https://github.com/WayScience/NF1_SchwannCell_data_analysis) for information on how the…

Orchestrating high-dimensional cell morphology data processing pipelines

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

The Zhang Lab Manual: Lab principles and activities, handbook for reproducible computational research, learning resources, expectations and achievements, etc

Source for the IDR static website.

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

Mondo Disease Ontology

Utility scripts for managing IDR submissions

Jupyter Notebooks for the Image Data Resource

Image-based Profiling Recipe