A survey of best practices for RNA-seq data analysis
Abstract RNA-sequencing (RNA-seq) has a wide variety of applications, but no single
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …
Mass cytometry: single cells, many features
MH Spitzer, GP Nolan - Cell, 2016 - cell.com
Technology development in biological research often aims to either increase the number of
cellular features that can be surveyed simultaneously or enhance the resolution at which …
cellular features that can be surveyed simultaneously or enhance the resolution at which …
[HTML][HTML] A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of
individual cells. This provides biological resolution that cannot be matched by bulk RNA …
individual cells. This provides biological resolution that cannot be matched by bulk RNA …
Pooling across cells to normalize single-cell RNA sequencing data with many zero counts
Normalization of single-cell RNA sequencing data is necessary to eliminate cell-specific
biases prior to downstream analyses. However, this is not straightforward for noisy single …
biases prior to downstream analyses. However, this is not straightforward for noisy single …
[HTML][HTML] Molecular diversity of midbrain development in mouse, human, and stem cells
G La Manno, D Gyllborg, S Codeluppi, K Nishimura… - Cell, 2016 - cell.com
Understanding human embryonic ventral midbrain is of major interest for Parkinson's
disease. However, the cell types, their gene expression dynamics, and their relationship to …
disease. However, the cell types, their gene expression dynamics, and their relationship to …
Revealing the vectors of cellular identity with single-cell genomics
Single-cell genomics has now made it possible to create a comprehensive atlas of human
cells. At the same time, it has reopened definitions of a cell's identity and of the ways in …
cells. At the same time, it has reopened definitions of a cell's identity and of the ways in …
Classification of low quality cells from single-cell RNA-seq data
Single-cell RNA sequencing (scRNA-seq) has broad applications across biomedical
research. One of the key challenges is to ensure that only single, live cells are included in …
research. One of the key challenges is to ensure that only single, live cells are included in …
Design and computational analysis of single-cell RNA-sequencing experiments
R Bacher, C Kendziorski - Genome biology, 2016 - Springer
Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary tool that allows
us to address scientific questions that eluded examination just a few years ago. With the …
us to address scientific questions that eluded examination just a few years ago. With the …
Single-cell analysis tools for drug discovery and development
The genetic, functional or compositional heterogeneity of healthy and diseased tissues
presents major challenges in drug discovery and development. Such heterogeneity hinders …
presents major challenges in drug discovery and development. Such heterogeneity hinders …
[HTML][HTML] Single-cell transcriptomics reveals that differentiation and spatial signatures shape epidermal and hair follicle heterogeneity
The murine epidermis with its hair follicles represents an invaluable model system for tissue
regeneration and stem cell research. Here we used single-cell RNA-sequencing to reveal …
regeneration and stem cell research. Here we used single-cell RNA-sequencing to reveal …