Deconer_dataset

Well-Characterized Cell-Type Deconvolution Datasets

This repository is a part of Deconer.

NO.	NAME	Description	Reference Type	Proportion	Sample Size	Source
1	Abbas	Microarray	Bulk	known	12	Abbas, et al.
2	Becht	Microarray	Bulk	known	10	Becht, et al.
3	Gong	Microarray	Bulk	known	9	Gong, et al.
4	Kuhn	Microarray	Bulk	known	10	Kuhn, et al.
5	Linsley	RNA-seq	Bulk	known	5	Linsley, et al.
6	Liu	RNA-seq	Bulk	known	24	Liu, et al.
7	Parsons	RNA-seq	Bulk	known	30	Parsons, et al.
8	Shen-Orr	Microarray	Bulk	known	33	Shen-Orr, et al.
9	Shi	Microarray	Bulk	known	60	Shi, et al.
10	T2D	RNA-seq	Single Cell	unknown	89	Fadista, et al.
11	TCGA_LUSC	RNA-seq	Bulk	unknown	130	Vasaikar, et al.
12	TCGA_OV	RNA-seq	Bulk	unknown	514	Vasaikar, et al.
13	kidney_Arvaniti	RNA-seq	Single Cell	unknown	11	Arvaniti, et al.
14	kidney_Arvaniti_TPM	RNA-seq	Bulk	unknown	11	Arvaniti, et al.
15	kidney_Craciun	RNA-seq	Single Cell	unknown	19	Craciun, et al.
16	kidney_Craciun_TPM	RNA-seq	Bulk	unknown	19	Craciun, et al.
17	TCGA 35 cancer datasets	RNA-seq	Bulk	unknown	-	Vasaikar, et al.

Folder ‘ClassificationAndSurvivalAnalysis_TCGA’ contains 35 cancer datasets from TCGA with clinical informations.

Note: some dataset are collected from dtangle and MuSiC.

Please cite the corresponding article when you use the datasets.

Zhang, Wei, et al. “Deconer: A comprehensive and systematic evaluation toolkit for reference-based cell type deconvolution algorithms using gene expression data.” bioRxiv (2023): 2023-12.

Links:

• Deconer
• Deconer manual
• Deconer vignettes
• Deconer datasets