humengying0907 / InstaPrism

InstaPrism is an R package for fast implementation of BayesPrism

InstaPrism

InstaPrism is R package to deconvolute cellular proportion and gene expression in bulk RNA-Seq data. Based on the same conceptual framework and corresponding generative mode from BayesPrism, InstaPrism re-implements BayesPrism in a derandomized framework by replacing the time-consuming Gibbs sampling steps in BayesPrism with a fixed-point algorithm, which greatly accelerated the calculation speed while maintaining highly comparable performance.

Installation

library("devtools");
install_github("humengying0907/InstaPrism")

Deconvolution results comparison with BayesPrism

Using either scRNA-based reference (update = F) or updated reference (update = T), InstaPrism achieves identical deconvolution results as BayesPrism.

Running time comparsion with BayesPrism

Below is a running time comparsion when running deconvolution on the tutorial data provided in BayesPrism.

Memory Comparison with BayesPrism

InstaPrism significantly reduced the memory required to store the deconvolution project, when running deconvolution on the tutorial data provided in BayesPrism.

Built-in Reference for InstaPrism

We have provided precompiled reference tailored for a wide range of cancer types. Download the reference from the link below and use the following code to run deconvolution.

# take BRCA_refPhi for example
BRCA_refPhi = readRDS("BRCA_refPhi.RDS")
InstaPrism.res = InstaPrism(input_type = 'refPhi_cs', bulk_Expr = bulk_expr,refPhi_cs = BRCA_refPhi, n.core = 16)

reference name	tumor type	#cells used for reference construction	#cell types/cell states	umap	citation	download
BRCA_refPhi	breast cancer	100,064	9/76	UMAP	Wu et al. 2021	↓
CRC_refPhi	colorectal cancer	371,223	15/149	UMAP	Pelka et al. 2021	↓
GBM_refPhi	glioblastoma	338,564	8/55	cellxgeneLink, UMAP	Ruiz et al. 2022	↓
LUAD_refPhi	lung adenocarcinomas	118,293	13/74	UMAP	Xing et al. 2021	↓
OV_refPhi	ovarian cancer	929,690	9/40	cellxgeneLink, UMAP	Vazquez et al. 2022	↓
RCC_refPhi	clear cell renal cell carcinoma	270,855	12/86	cellxgeneLink, UMAP	Li et al. 2022	↓
SKCM_refPhi	skin cutaneous melanoma	4,645	8/23	UMAP	Tirosh et al. 2016	↓

Tutorial

Check InstaPrism_tumorial for detailed implementation of InstaPrism and compare its performance with BayesPrism.

Reference

M. Hu and M. Chikina, “InstaPrism: an R package for fast implementation of BayesPrism.” bioRxiv, p. 2023.03.07.531579, Mar. 12, 2023. doi: https://doi.org/10.1101/2023.03.07.531579