Data for "Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis"

The files named <code>df_scran.csv</code>, <code>df_seurat.csv</code>, <code>df_zinbwave.csv</code>, <code>df_dca.csv</code>, and <code>df_scvi.csv</code> contain one row per configuration that we ran successfully. The files named <code>DATASET.METHOD.h5ad</code> are encoded with anndata <code>v0.7.0</code> (be careful as they are not readable with previous versions) and contain 100 embeddings each. The embeddings are in the <code>obsm</code> attribute of the object. All the embeddings can be listed with the <code>obsm_keys()</code> method. The name of the embedding contains the parameters used to generate that embedding and are written like that <code>method=zinbwave.dims=10.epsilon=1000.features=300.gene_covariate=0</code>. For questions on this dataset please contact [e-mail]