Python Jupyter notebooks for BioImageAnalysis, GPU-accelerated image processing, bio-image data science and more

Deep Learning Library for Single Cell Analysis

An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.

Biomni: a general-purpose biomedical AI agent

napari: a fast, interactive, multi-dimensional image viewer for python

Code for IN-DEPTH

Spatial Partitioning of Tumor- Immune Architecture via Multi-omics), an open-source computational framework that integrates genomic, transcriptomic, and proteomic data at single-cell resolution to …

Easily create a beautiful website using Academic and Hugo

An open and interoperable data framework for spatial omics data

CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots

Probabilistic cell segmentation for in situ spatial transcriptomics

The Fast Cross-Platform Package Manager

Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"

A package to help convert different single-cell data formats to each other

Reader of R datasets in .rda format, in Python

你今天读论文了吗

StarDist - Object Detection with Star-convex Shapes

Infer Copy Number Alterations and Clonality in (Single-Cell) RNA-Seq Data

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

CNA Simulator for scRNA-seq data

Create thumbnails of cells in a given image.

HKU Thesis Template

CSPOT: A scalable framework for automated processing of highly multiplexed tissue images

modular in structure; chapters separated into separate source files with cross-referencing (with hyperlinks) enabled