LARRY-dataset 0.0.1

LARRY Dataset: lineage and RNA recovery

LARRY dataset

Installation

pip distribution

pip install larry-dataset

Development version

git clone https://github.com/mvinyard/LARRY-dataset.git; cd LARRY-dataset

pip install -e .

Quickstart

Downloads pre-processed data from AllonKleinLab/paper-data to ./KleinLabData (by default). The data is formatted into AnnData and returned to the user. A .h5ad file is also saved, locally. The data downloading and conversion step take several minutes due to the large expression normed_counts matrices though this only happens once.

import larry
    
dataset = "in_vitro" # can also choose from: "in_vivo" or "cytokine_perturbation"
adata = larry.fetch(dataset)

AnnData object with n_obs × n_vars = 130887 × 25289
    obs: 'Library', 'Cell barcode', 'Time point', 'Starting population', 'Cell type annotation', 'Well', 'SPRING-x', 'SPRING-y'
    var: 'gene_name'
    obsm: 'X_clone'

import larry

LARRY_LightningData = larry.LARRY_LightningDataModule()
LARRY_LightningData.prepare_data()

 AnnData object with n_obs × n_vars = 130887 × 25289
    obs: 'Library', 'Cell barcode', 'Time point', 'Starting population', 'Cell type annotation', 'Well', 'SPRING-x', 'SPRING-y'
    var: 'gene_name'
    uns: 'dataset', 'h5ad_path'
    obsm: 'X_clone'
Preprocessing performed previously. Loading...done.

Under the hood, the LARRY_LightningData calls larry.fetch() and larry.pp.Yeo2021_recipe(), and if task == "fate_prediction", larry.pp.annotate_fate_test_train()

LARRY_LightningData.adata

Print the updated adata:

AnnData object with n_obs × n_vars = 130887 × 25289
    obs: 'Library', 'Cell barcode', 'Time point', 'Starting population', 'Cell type annotation', 'Well', 'SPRING-x', 'SPRING-y', 'cell_idx', 'clone_idx'
    var: 'gene_name', 'highly_variable', 'corr_cell_cycle', 'pass_filter'
    uns: 'dataset', 'h5ad_path', 'highly_variable_genes_idx', 'n_corr_cell_cycle', 'n_hv', 'n_mito', 'n_pass', 'n_total', 'pp_h5ad_path'
    obsm: 'X_clone', 'X_pca', 'X_scaled', 'X_umap'

Sources

Repositories

• AllonKleinLab/paper-data
• AllonKleinLab/LARRY

Reference

• Weinreb, C., Rodriguez-Fraticelli, A., Camargo, F.D., Klein, A.M. Lineage tracing on transcriptional landscapes links state to fate during differentiation. Science 80 (2020). https://doi.org/10.1126/science.aaw3381

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Please email Michael E. Vinyard ([e-mail]) with any questions or interests.