Improved cell composition deconvolution method of bulk gene expression profiles to quantify subsets of immune cells

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

(2019) Xuran Wang et al.   Nature Communications

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types

(2019) Gianni Monaco et al.   Cell Reports

Estimation of immune cell content in tumor using single-cell RNA-seq reference data

(2019) Xiaoqing Yu et al.   BMC CANCER

Ten quick tips for effective dimensionality reduction

(2019) Lan Huong Nguyen et al.   PLoS Computational Biology

Quantifying tumor-infiltrating immune cells from transcriptomics data

(2018) Francesca Finotello et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Macrophages as Key Drivers of Cancer Progression and Metastasis

(2017) Sebastian R. Nielsen et al.   MEDIATORS OF INFLAMMATION

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade

(2017) Pornpimol Charoentong et al.   Cell Reports

Analysis of distinct long noncoding RNA transcriptional fingerprints in pancreatic ductal adenocarcinoma

(2017) Xiang Yu et al.   Cancer Medicine

Regulatory T cells, especially ICOS+ FOXP3+ regulatory T cells, are increased in the hepatocellular carcinoma microenvironment and predict reduced survival

(2016) Jian-Fei Tu et al.   Scientific Reports

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples

(2013) David A. Liebner et al.   BIOINFORMATICS

Digital sorting of complex tissues for cell type-specific gene expression profiles

(2013) Yi Zhong et al.   BMC BIOINFORMATICS

PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions

(2012) Wenlian Qiao et al.   PLoS Computational Biology

Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: A case study

(2011) Renaud Gaujoux et al.   INFECTION GENETICS AND EVOLUTION

Optimal Deconvolution of Transcriptional Profiling Data Using Quadratic Programming with Application to Complex Clinical Blood Samples

(2011) Ting Gong et al.   PLoS One

Statistical expression deconvolution from mixed tissue samples

(2010) J. Clarke et al.   BIOINFORMATICS

Correlation, Agreement, and Bland–Altman Analysis: Statistical Analysis of Method Comparison Studies

(2009) Catey Bunce   AMERICAN JOURNAL OF OPHTHALMOLOGY

Deconvolution of Blood Microarray Data Identifies Cellular Activation Patterns in Systemic Lupus Erythematosus

(2009) Alexander R. Abbas et al.   PLoS One

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS