This repository stores the steps used to generate the AIFI Immune Health Atlas dataset based on 10x 3' scRNA-seq data. There are 6 major stages to this process. Each stage is stored in a subdirectory in this repository:
01-Sample_selection: Sample selection and retrieval02-Reference_Labeling: Labeling with public references03-Subclustering: Separating major classes and subclustering04-Annotation: Expert annotation of cell type identity of each cluster05-Assembly: Assembly of annotations and final reference dataset06-Modeling: Generation of cell type labeling models using CellTypist
These notebooks can be run sequentially based on their numeric prefix. They are also prefixed by the language/notebook kernel used in each (Python or R), as both languages are utilized in this analysis.
Qiuyu Gong: Analysis lead, composed most original notebook versions
Lucas Graybuck: Review, documentation, linting, and reproducibility management
Xiao-jun Li: Analysis oversight
Mehul Sharma: Original version of 07a-Python_B_cells_without_Igs.ipynb
Aishwarya Chander: Annotation contributor; Ontology lead
Marla Glass: B cell annotation lead
Claire Gustafson: Scientific lead; T cell annotation lead
Emma Kuan: Myeloid cell annotation lead
Tao Peng: NK cell annotation lead
Mehul Sharma: B cell Annotation contributor
Mansi Singh: Myeloid cell annotation contributor
The license for this package is available on Github in the file LICENSE.txt in this repository.
We are not currently supporting this code, but simply releasing it to the community AS IS but are not able to provide any guarantees of support. The community is welcome to submit issues, but you should not expect an active response.
If you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in the file CONTRIBUTING.md in this repository.