This website outlines the key tools and software packages developed from my research:
- FASTQ+: This format enhances the standard FASTQ file by integrating barcode information directly into the read name. This modification facilitates the harmonization of single-cell sequencing data across various platforms. FASTQ+ can be generated with PISA.
- PISA: A suite of programs specifically designed for preprocessing data from single-cell sequencing and spatial transcriptomics. It efficiently processes FASTQ+, BAM, and BED files, streamlining the handling and generates various feature counts, facilitating the downstream analyses necessary for in-depth biological insights.
- Yano: An R package that employs the spatial dissimilarity test method as its core algorithm. Yano is tailored for exploring various biological events in single-cell data, including alternative splicing, allele-specific gene expression, and more, providing comprehensive insights into cellular dynamics.
Workflows
- From raw reads to gene counts (PISA)
- Alternative splicing analysis for scRNA-seq (PISA + Seurat + Yano)
- Allele-specific gene expression analysis for scRNA-seq (PISA + Seurat + Yano)
- Annotate and visualise genetic varaints for scRNA-seq (Yano)
- Prioritize non-exonic reads in scRNA-seq (PISA + Seurat + Yano)