scAnalysisPractice

reading_file_formats.ipynb

Data:

1. Ependymal cells (RDS): https://dataverse.harvard.edu/file.xhtml?persistentId=doi%3A10.7910%2FDVN%2FQB5CC8%2FCTZB3R&version=1.0
2. Seurat Obj (hdf5): 10x genomics 20k_PBMC_3p_HT_nextgem_Chromium_X_filtered_feature_bc_matrix.h5
3. Feature barcode matrix: 10x genomics 20k_PBMC_3p_HT_nextgem_Chromium_X_raw_feature_bc_matrix/raw_feature_bc_matrix/matrix.mtx.gz

nsclc.ipynb

Data: https://www.10xgenomics.com/datasets/20-k-mixture-of-nsclc-dt-cs-from-7-donors-3-v-3-1-3-1-standard-6-1-0
QC, filtering, normalize, feature selection