popsicleR

popsicleR performs pre-processing and quality control of single-cell RNA-seq (scRNA-seq) data, including estimation of quality-control metrics, filtering of low-quality cells, normalization, and removal of technical and biological biases, and accepts Cell Ranger (10X Genomics) outputs or feature-barcode matrices of raw counts to prepare data for downstream clustering and annotation.

Key Features:

• Quality-control metrics estimation: Calculates metrics to assess the quality of individual cells and overall scRNA-seq datasets.
• Low-quality cell filtering: Identifies and removes low-quality cells based on computed QC metrics.
• Normalization: Standardizes expression levels across samples to mitigate batch effects and sample-to-sample variability.
• Removal of technical and biological biases: Implements methods to remove unwanted sources of variation from expression data.
• Integration of established methods: Incorporates approaches from recognized pipelines for QC, filtering, normalization, and bias correction.
• Pre-processing workflow wrappers: Provides wrapper functions to execute the main pre-processing steps in a cohesive workflow.
• Cell clustering and annotation: Supports downstream cell clustering and annotation on processed data.
• Compatibility with multiple input formats: Accepts outputs from the Cell Ranger pipeline by 10X Genomics and feature-barcode matrices of raw counts from any scRNA-seq technology.

Scientific Applications:

• Exploration of cellular heterogeneity: Enables analysis of cell-to-cell variation within tissues and samples using high-quality scRNA-seq data.
• Cell type identification and annotation: Facilitates discovery and annotation of distinct cell types from processed single-cell datasets.
• Gene expression analysis at single-cell resolution: Supports investigation of gene expression patterns and differential expression analyses after QC and normalization.

Methodology:

The package calculates quality-control metrics, filters low-quality cells, performs normalization, and removes technical and biological sources of variation.