SAVER: gene expression recovery for single-cell RNA sequencing
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 …
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
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 …
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
The emerging single-cell RNA sequencing (scRNA-seq) technologies enable the
investigation of transcriptomic landscapes at the single-cell resolution. ScRNA-seq data …
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
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 …
profiling transcriptomes of hundreds to thousands of single cells. This technology has led to …
Comparative analysis of sequencing technologies for single-cell transcriptomics
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 …
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
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 …
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
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 …
and allelic expression across cell types and states. However, current short-read single-cell …
DrImpute: imputing dropout events in single cell RNA sequencing data
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 …
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
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 …
hundreds or thousands of cells after amplification of the cDNA. The high throughput is made …
Optimized single-nucleus transcriptional profiling by combinatorial indexing
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 …
recovering gene expression data from an exponentially scalable number of individual cells …