datasetScoresHuman: datasetScoresHuman

In SysBioChalmers/DSAVE-R: DSAVE: Tools to Investigate Variation and Purity of Subpopulations in Single-Cell RNA-Seq Data

Description

DSAVE scores from public datasets evaluated with the standard template. Can be used for comparison against the score generated to see if it is comparable to scores from other datasets.

Usage

datasetScoresHuman

Format

list of lists, where the inner list contains the dataset name (as named in the DSAVE publication) and the DSAVE score.

Source

Calculated with the DSAVE-M package in MATLAB, but the results should be the same.

BC	Azizi, E. et al. Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment. Cell (2018). doi:10.1016/j.cell.2018.05.060.	50/50 mix of T cells from the two samples 'BC1_BLOOD' and 'BC4_BLOOD' from the BC dataset, in total 3,532 cells.
OC	Schelker, M. et al. Estimation of immune cell content in tumour tissue using single-cell RNA-seq data. Nat. Commun. 8, 2032 (2017).	All macrophages from the OC dataset, in total 2,057 cells.
LC	Lambrechts, D. et al. Phenotype molding of stromal cells in the lung tumor microenvironment. Nat. Med. 24, 1277–1289 (2018).	All t cells from the healthy tissue of patient 3, 4 and 5 from the LC dataset, in total 3,471 cells.
LIVC	Zheng, C. et al. Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing. Cell 169, 1342-1356.e16 (2017).	All cells from the LIVC dataset, in total 4,070 cells. Note that UMIs are not used for this dataset, which could explain the higher variation.
PBMC68k	Zheng, G. X. Y. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).	~68,000 T cells. All T cells from the PBMC68k dataset, in total 48,657 cells.
B10k	Zheng, G. X. Y. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).	~10,000 FACS-sorted B cells (CD19+). All cells from the B10k dataset, in total 10,085 cells.
CD4TMEM	Zheng, G. X. Y. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).	~10,000 FACS-sorted CD4+ T memory cells. All cells from the CD4TMEM dataset, in total 10,224 cells.
HCA CB	Li, B. et al. Census of Immune Cells. Human Cell Atlas Data Portal (2018).	All T cells from patient 'CB1', 'CB2' and 'CB3' from the HCA CB dataset, in total 30,462 cells.
CD8T	Chen, J. et al. PBMC fixation and processing for Chromium single-cell RNA sequencing. J. Transl. Med. 16, 198 (2018).	All cells from the TCD8 dataset, in total 5,662 cells.

SysBioChalmers/DSAVE-R documentation built on Oct. 19, 2021, 11:37 p.m.