influenza-a

Transcriptomic profiling pipeline for quantifying multi-segment Influenza A (H1N1) viral gene expression from RNA-seq data using Bowtie2 and R.

Reference-guided genomic variant mapping pipeline and intrahost variome atlas for the segmented Influenza A virus (H1N1pdm09), characterizing within-host quasispecies diversity and mutational burdens using deep sequence data.

Influenza antiviral resistance interpretation pipeline using amino acid sequences and WHO mutation rules.

Python CLI that detects entity leakage, reversed-role leakage, and temporal overclaiming in influenza antigenicity evaluations.

HA Cleavage Site Finder is a bioinformatics workflow developed to identify cleavage sites in the hemagglutinin gene of the influenza A virus (IA) and infer its pathogenicity. The database used for prediction is based on the latest version (2022, to date) of: OFFLU. (2022). Influenza A Cleavage Sites. Version 4th January 2022.