data-natcom2020/README.md

In jmonlong/scCNAutils: Functions to analyze copy number aberrations in single-cell data

The code from this package was written and used primarily for the following study.

Couturier, C.P., Ayyadhury, S., Le, P.U. et al. Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy. Nat Commun 11, 3406 (2020). https://doi.org/10.1038/s41467-020-17186-5

The list of cancer/non-cancer cells are available in the cells-community-normal-natcom2020.tsv.gz. This tsv has three columns: the sample ID, the barcode of the cell, and the community name (in the form of <SAMPLE>.<CLONE>, or normal for non-cancer cells).

sample  barcode community.patient
BT402_W ATCATCTTCTTCCTTC-1  normal
BT363_W CATCGGGAGTCATCCA-1  BT363.1
BT326_GSC   ACGCCGAAGCGATAGC-1  BT326.2
...

jmonlong/scCNAutils documentation built on Feb. 8, 2025, 8:09 a.m.