(NOTE: This is a development fork, please refer to official repo at statgen: https://github.com/statgen/popscle) Freemuxlet methods and auxilary tools
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Updated
Oct 28, 2019 - C++
(NOTE: This is a development fork, please refer to official repo at statgen: https://github.com/statgen/popscle) Freemuxlet methods and auxilary tools
Website for the fibroblast clonality project conducted at EMBL-EBI and the Wellcome Sanger Institute ca 2017-2019.
Single-Cell Data Science
Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments
It contains the functional code to analyze P2 scRNA-seq and scATAC-seq data.
The software of Pamona, a partial manifold alignment algorithm.
A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools
A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍
R Shiny app for Vitessce, an integrative and interactive data visualization tool for exploration of spatial single-cell experiments.
Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
R Package for Single-Cell Dataset Processing and Visualization
Documentation analysis and manuscript figures of QuRIE-seq methods paper.
Pytorch implementation of "Multi-domain translation between single-cell imaging and sequencing data using autoencoders" (https://www.nature.com/articles/s41467-020-20249-2) with custom models.
Code for Jonsson*, Zhang*, et al, TteK (Granzyme K+ CD8 T cells), Science Translational Medicine, 2022: the core population of inflamed human tissue-associated CD8 T cells.
Papers and Tools that would guide your journey in Computational Biochemistry
Documentation analysis and manuscript figures
resVAE is a restricted latent variational autoencoder that we wrote to uncover hidden structures in gene expression data, especially using single-cell RNA sequencing. In principle it can be used with any hierarchically structured data though, so feel free to play around with it.
As part of the IEE Healthcare Summit Data Hackathon(2022) Challenge designed a classification model to predict severity of COVID-19 infection from scRNA-seq data.
Repository for projects in Single Cell
Analysis code for the clue framework paper: efficient pooled single-cell sequencing without reference genotypes.
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