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Use dimensionality reduction to create thumnails for high-dimensional imaging
Library with some less common or extended spatial functions
Segment Anything for Microscopy
A module with convenience functions for writing Python code that interacts with OMERO.
High performance rasterization tool for Python 🐍 built in Rust 🦀
STUMPY is a powerful and scalable Python library for modern time series analysis
Enhanced stain normalization for histopathology images with batch processing support. Optimized for CPU, GPU (CUDA), and MPS (Apple Silicon) devices.
We write your reusable computer vision tools. 💜
A GPU-accelerated web application for visualization, annotation and sharing of spatial biology data
C++ whole slide image reader with native python bindings
A Python toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.
Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
Workflow to Fetch Public Sequencing Data and Metadata Using iSeq and MrBiomics Module.
RNA-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e…
A Snakemake workflow and MrBiomics module for performing and visualizing differential analyses of NGS data powered by the R package limma.
A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.
A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the packa…
A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Se…
A general purpose Snakemake workflow and MrBiomics module to perform unsupervised analyses (dimensionality reduction & cluster analysis) and visualizations of high-dimensional data.
A Snakemake workflow and MrBiomics module for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) powered by the R package Seurat's meth…
A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
Domain-specific language designed to streamline the development of high-performance GPU/CPU/Accelerators kernels
scDataset: Scalable Data Loading for Deep Learning on Large-Scale Single-Cell Omics