FD-seq

Fixed single-cell RNA sequencing for understanding virus infection and host response

This repository store the code used to align sequencing data, and analyze count data.

Species-mixing data

• alignment folder: alignment code.
• mix_species_analysis.py: analysis of species mixing data.

Technical replicates data

• alignment folder: alignment code.
• data_analysis.R: normalization and analysis of technical replicates data.

KSHV data

• alignment folder: alignment code.
• Van_analysis_monocle_20200819.R: analysis of FD-seq single-cell data.
• viral_gene_correlation.py: calculate correlation among viral genes from FD-seq single-cell data.
• data_analysis.py: analysis of fluorescence intensity data.
• data_analysis_v3.py: analysis of qPCR data.

OC43 data

• alignment folder: alignment code.
• 20200630.R: analysis of FD-seq single-cell data.
• plot_data.py: additional plotting of FD-seq single-cell data.

RNA velocity analysis

• RNA velocity commands.txt: get spliced and unspliced count data using dropEst.
• positive_velocyto.loom and negative_velocyto.loom: spliced and unspliced count data.
• Van_analysis_loom.py: plotting of data processed by velocyto.