Orchestrating single-cell analysis with Bioconductor

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

(2019) Tianyu Wang et al.   BMC BIOINFORMATICS

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments

(2019) Luyi Tian et al.   NATURE METHODS

scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data

(2019) Zhe Wang et al.   BMC BIOINFORMATICS

scds: computational annotation of doublets in single-cell RNA sequencing data

(2019) Abha S Bais et al.   BIOINFORMATICS

Reproducible and replicable comparisons using SummarizedBenchmark

(2018) Patrick K Kimes et al.   BIOINFORMATICS

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data

(2018) Shun H Yip et al.   BRIEFINGS IN BIOINFORMATICS

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data

(2018) Jean Fan et al.   GENOME RESEARCH

Identifying cell populations with scRNASeq

(2018) Tallulah S. Andrews et al.   MOLECULAR ASPECTS OF MEDICINE

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

SAVER: gene expression recovery for single-cell RNA sequencing

(2018) Mo Huang et al.   NATURE METHODS

Bias, robustness and scalability in single-cell differential expression analysis

(2018) Charlotte Soneson et al.   NATURE METHODS

Detection and removal of barcode swapping in single-cell RNA-seq data

(2018) Jonathan A. Griffiths et al.   Nature Communications

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA

(2018) K. G. Paulson et al.   Nature Communications

Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq

(2018) Mihriban Karaayvaz et al.   Nature Communications

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data

(2018) Luyi Tian et al.   PLoS Computational Biology

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets

(2018) Davide Risso et al.   PLoS Computational Biology

M3Drop: dropout-based feature selection for scRNASeq

(2018) Tallulah S Andrews et al.   BIOINFORMATICS

The Human Cell Atlas: from vision to reality

(2017) Orit Rozenblatt-Rosen et al.   NATURE

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Normalizing single-cell RNA sequencing data: challenges and opportunities

(2017) Catalina A Vallejos et al.   NATURE METHODS

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data

(2016) David A. duVerle et al.   BMC BIOINFORMATICS

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis

(2016) Ludwig Geistlinger et al.   BMC BIOINFORMATICS

Computational methods for trajectory inference from single-cell transcriptomics

(2016) Robrecht Cannoodt et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq

(2016) Iain C Macaulay et al.   Nature Protocols

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Next-generation sequencing: advances and applications in cancer diagnosis

(2016) Simona Serratì et al.   OncoTargets and Therapy

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

(2014) Martin J. Aryee et al.   BIOINFORMATICS

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Object-Oriented Programming, Functional Programming and R

(2014) John M. Chambers   STATISTICAL SCIENCE

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments

(2012) Andrew McDavid et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS