Readings for Context

Recommended Reading Order

1. Get key highlights:
   1. Box 1 of Current best practices in single‐cell RNA‐seq analysis: a tutorial
   2. Pages 14 - 16 of User Guide - Chromium Single Cell 3’ Reagent Kits V3
   3. Figure 2 of Comparative Analysis of Single-Cell RNA Sequencing Methods
2. Read more details:
   1. Current best practices in single‐cell RNA‐seq analysis: a tutorial
   2. Comparative Analysis of Single-Cell RNA Sequencing Methods
   3. Massively parallel digital transcriptional profiling of single cells

Relevant Readings by Topic

For single cell RNA sequencing (scRNA-seq):

• User Guide - Chromium Single Cell 3’ Reagent Kits V3 - Pages 14 to 16
• Technology and Biology of Single-Cell RNA Sequencing
• Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets

For comparative analyses of scRNA-seq:

• Current best practices in single‐cell RNA‐seq analysis: a tutorial
• Comparative Analysis of Single-Cell RNA Sequencing Methods
• A systematic evaluation of single cell RNA-seq analysis pipelines
• A comparison of single-cell trajectory inference methods

For scRNA-seq analysis pipelines:

• Massively parallel digital transcriptional profiling of single cells

For cell trajectory analysis:

• PAGA - graph abstraction reconciles clustering with trajectory inference
• Revealing the vectors of cellular identity with single-cell genomics
• SPRING: a kinetic interface for visualizing high dimensional single-cell expression data

For Nanopore sequencing:

• Efficient de novo assembly of eleven human genomes using PromethION and a novel nanopore toolkit

For Data Analysis:

• Gene Set Enrichment Analysis

For File Formats:

• Matrix Market File Format
• HDF5 VOL docs