DISCO: a database of Deeply Integrated human Single-Cell Omics data

Single-cell multi-omics analysis of the immune response in COVID-19

(2021) Emily Stephenson et al.   NATURE MEDICINE

Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia

(2021) Ugomma C. Eze et al.   NATURE NEUROSCIENCE

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

GSA: Genome Sequence Archive *

(2017) Yanqing Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

(2016) Alexander D. Diehl et al.   Journal of Biomedical Semantics

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Modeling sample variables with an Experimental Factor Ontology

(2010) James Malone et al.   BIOINFORMATICS