SAVER: gene expression recovery for single-cell RNA sequencing

M Huang, J Wang, E Torre, H Dueck, S Shaffer… - Nature …, 2018 - nature.com
In single-cell RNA sequencing (scRNA-seq) studies, only a small fraction of the transcripts
present in each cell are sequenced. This leads to unreliable quantification of genes with low …

Batch effects and the effective design of single-cell gene expression studies

PY Tung, JD Blischak, CJ Hsiao, DA Knowles… - Scientific reports, 2017 - nature.com
Single-cell RNA sequencing (scRNA-seq) can be used to characterize variation in gene
expression levels at high resolution. However, the sources of experimental noise in scRNA …

An accurate and robust imputation method scImpute for single-cell RNA-seq data

WV Li, JJ Li - Nature communications, 2018 - nature.com
The emerging single-cell RNA sequencing (scRNA-seq) technologies enable the
investigation of transcriptomic landscapes at the single-cell resolution. ScRNA-seq data …

[HTML][HTML] Gene length and detection bias in single cell RNA sequencing protocols

B Phipson, L Zappia, A Oshlack - F1000Research, 2017 - ncbi.nlm.nih.gov
Background: Single cell RNA sequencing (scRNA-seq) has rapidly gained popularity for
profiling transcriptomes of hundreds to thousands of single cells. This technology has led to …

Comparative analysis of sequencing technologies for single-cell transcriptomics

KN Natarajan, Z Miao, M Jiang, X Huang, H Zhou, J Xie… - Genome Biology, 2019 - Springer
Single-cell RNA-seq technologies require library preparation prior to sequencing. Here, we
present the first report to compare the cheaper BGISEQ-500 platform to the Illumina HiSeq …

A systematic evaluation of single cell RNA-seq analysis pipelines

B Vieth, S Parekh, C Ziegenhain, W Enard… - Nature …, 2019 - nature.com
The recent rapid spread of single cell RNA sequencing (scRNA-seq) methods has created a
large variety of experimental and computational pipelines for which best practices have not …

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

M Hagemann-Jensen, C Ziegenhain, P Chen… - Nature …, 2020 - nature.com
Large-scale sequencing of RNA from individual cells can reveal patterns of gene, isoform
and allelic expression across cell types and states. However, current short-read single-cell …

DrImpute: imputing dropout events in single cell RNA sequencing data

W Gong, IY Kwak, P Pota, N Koyano-Nakagawa… - BMC …, 2018 - Springer
Background The single cell RNA sequencing (scRNA-seq) technique begin a new era by
allowing the observation of gene expression at the single cell level. However, there is also a …

[PDF][PDF] zUMIs-A fast and flexible pipeline to process RNA sequencing data with UMIs

S Parekh, C Ziegenhain, B Vieth, W Enard… - …, 2018 - academic.oup.com
Background Single-cell RNA-sequencing (scRNA-seq) experiments typically analyze
hundreds or thousands of cells after amplification of the cDNA. The high throughput is made …

Optimized single-nucleus transcriptional profiling by combinatorial indexing

BK Martin, C Qiu, E Nichols, M Phung… - Nature protocols, 2023 - nature.com
Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for
recovering gene expression data from an exponentially scalable number of individual cells …