This is the pipeline to perform a Drop-seq simulation based benchmark - see https://www.biorxiv.org/content/early/2018/01/17/248716
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Updated
Jul 25, 2018 - Shell
This is the pipeline to perform a Drop-seq simulation based benchmark - see https://www.biorxiv.org/content/early/2018/01/17/248716
Benchmarking pipeline published in https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1571-5
Benchmarking pipeline published in https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1571-5
Index and search single cell data.
Discrete Distributional Differential Expression
Distributed processing with NumPy and Zarr
Code for the empty droplet and cell detection project from the HCA Hackathon.
HumanCellAtlas upload-service validator for SpaceTx files
Experiments to run single cell analyses efficiently at scale using Zarr, anndata, Scanpy, and Apache Spark
Convert supported filesets to the SpaceTx format
This repository contains our CellTag CloneHunter R package for clone-calling.
This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.
Examples of custom panels for the iSEE package
Binary Factor Analysis: a dimensionality reduction tool for noisy, high throughput single cell genomic data
This contains the dataset for comparing scRNA-seq analysis methods
A tool for unsupervised projection of single cell RNA-seq data
A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
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