AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

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

Cell composition analysis of bulk genomics using single-cell data

(2019) Amit Frishberg et al.   NATURE METHODS

Determining cell type abundance and expression from bulk tissues with digital cytometry

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

deconvSeq: Deconvolution of Cell Mixture Distribution in Sequencing Data

(2019) Rose Du et al.   BIOINFORMATICS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures

(2019) Konstantin Zaitsev et al.   Nature Communications

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Allergic inflammatory memory in human respiratory epithelial progenitor cells

(2018) Jose Ordovas-Montanes et al.   NATURE

dtangle: accurate and robust cell type deconvolution

(2018) Gregory J Hunt et al.   BIOINFORMATICS

A test metric for assessing single-cell RNA-seq batch correction

(2018) Maren Büttner et al.   NATURE METHODS

Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases

(2018) Francesco Vallania et al.   Nature Communications

Estimation of immune cell content in tumour tissue using single-cell RNA-seq data

(2017) Max Schelker et al.   Nature Communications

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes

(2016) Åsa Segerstolpe et al.   Cell Metabolism

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

(2015) Olivia Padovan-Merhar et al.   MOLECULAR CELL

Respiratory epithelial cells orchestrate pulmonary innate immunity

(2015) Jeffrey A Whitsett et al.   NATURE IMMUNOLOGY

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Computational deconvolution: extracting cell type-specific information from heterogeneous samples

(2013) Shai S Shen-Orr et al.   CURRENT OPINION IN IMMUNOLOGY

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Cell population-specific expression analysis of human cerebellum

(2012) Alexandre Kuhn et al.   BMC GENOMICS

Collinearity: a review of methods to deal with it and a simulation study evaluating their performance

(2012) Carsten F. Dormann et al.   ECOGRAPHY

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

Population-specific expression analysis (PSEA) reveals molecular changes in diseased brain

(2011) Alexandre Kuhn et al.   NATURE METHODS

Applying unmixing to gene expression data for tumor phylogeny inference

(2010) Russell Schwartz et al.   BMC BIOINFORMATICS

Cell type–specific gene expression differences in complex tissues

(2010) Shai S Shen-Orr et al.   NATURE METHODS

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT