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Starred repositories
Integrated pipeline for multiplexed image analysis
SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network
Book about interpretable machine learning
Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
Deep Learning Library for Single Cell Analysis
napari: a fast, interactive, multi-dimensional image viewer for python
Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly multiplexed immunohistochemistry data. Docs available here: ht…
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
A system-level, binary package and environment manager running on all major operating systems and platforms.
Portfolio analytics for quants, written in Python
stefan-jansen / zipline-reloaded
Forked from quantopian/ziplineZipline, a Pythonic Algorithmic Trading Library
Portfolio and risk analytics in Python
BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics analysis.
LIANA+: an all-in-one framework for cell-cell communication
Linux virtual machines, with a focus on running containers
Singularity has been renamed to Apptainer as part of us moving the project to the Linux Foundation. This repo has been persisted as a snapshot right before the changes.
Official git repository for Biopython (originally converted from CVS)
A novel machine learning pipeline to analyse spatial transcriptomics data
Fast, sensitive and accurate integration of single-cell data with Harmony
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
Somatic structural variant caller for long-read data
Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)
An awesome LaTeX resume template to jumpstart your job search!