Stars
The bridge between the NCBI Gene Expression Omnibus and Bioconductor
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)
numfocus / MOSS
Forked from eyermt/mossMap 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
An open source extension that connects AI agents to computational notebooks in 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
A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin