Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

(2020) Xiaojie Qiu et al.   Cell Systems

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics

(2020) Simon Cabello-Aguilar et al.   NUCLEIC ACIDS RESEARCH

Untangling the effects of cellular composition on coexpression analysis

(2020) Marjan Farahbod et al.   GENOME RESEARCH

A single-cell transcriptomic atlas of the developing chicken limb

(2019) Christian Feregrino et al.   BMC GENOMICS

Evaluating measures of association for single-cell transcriptomics

(2019) Michael A. Skinnider et al.   NATURE METHODS

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

(2019) Christopher S. Smillie et al.   CELL

A field guide for the compositional analysis of any-omics data

(2019) Thomas P Quinn et al.   GigaScience

The effect of tissue composition on gene co-expression

(2019) Yun Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Reconstruction of Cell-type-Specific Interactomes at Single-Cell Resolution

(2019) Shahin Mohammadi et al.   Cell Systems

Mapping gene regulatory networks from single-cell omics data

(2018) Mark W E J Fiers et al.   Briefings in Functional Genomics

Continuous Variation within Cell Types of the Nervous System

(2018) Mark S. Cembrowski et al.   TRENDS IN NEUROSCIENCES

Variation among intact tissue samples reveals the core transcriptional features of human CNS cell classes

(2018) Kevin W. Kelley et al.   NATURE NEUROSCIENCE

Co-expression in Single-Cell Analysis: Saving Grace or Original Sin?

(2018) Megan Crow et al.   TRENDS IN GENETICS

TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information

(2017) Shubhada R Kulkarni et al.   NUCLEIC ACIDS RESEARCH

Complex Sources of Variation in Tissue Expression Data: Analysis of the GTEx Lung Transcriptome

(2016) Matthew N. McCall et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A transcription factor hierarchy defines an environmental stress response network

(2016) L. Song et al.   SCIENCE

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data

(2012) A. Zoubarev et al.   BIOINFORMATICS

Quality of Computationally Inferred Gene Ontology Annotations

(2012) Nives Škunca et al.   PLoS Computational Biology

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Coexpression network analysis of neural tissue reveals perturbations in developmental processes in schizophrenia

(2010) A. Torkamani et al.   GENOME RESEARCH