Repositories list

• global_genomic_surveillance_spatpomp_article

  Public
  Public repository for the project of modelling global genomic surveillance effectiveness.

  R

  •0•0•0•0•Updated Aug 27, 2025Aug 27, 2025

• GenEpi-HRI-HK-2022

  Public
  Genomic epidemiology analysis of hospital related infections in Hong Kong, 2022

  R

  •0•0•0•0•Updated May 14, 2025May 14, 2025

• Replication-defective-SARS-CoV-2-mutants

  Public
  This repository host the scripts and data used for designing genomic sequences of replication-defective SARS-CoV-2 mutants.

  R

  •0•0•0•0•Updated May 9, 2025May 9, 2025

• GEII

  Public
  host Gene Expression under Influenza virus infection or Interferon stimulation (GEII)

  Python

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• Lab-meeting-calendar

  Public
  0•0•0•0•Updated Nov 22, 2024Nov 22, 2024

• USP30-AS1-regulates-antiviral-immunity

  Public
  An Interferon-stimulated long non-coding RNA USP30-AS1 regulates antiviral immunity in influenza virus infection

  0•0•0•0•Updated Sep 26, 2024Sep 26, 2024

• Astrovirus

  Public
  0•0•0•0•Updated Jun 20, 2024Jun 20, 2024

• analysis-Influenza-antibody-subclass-and-effector-functions

  Public
  Influenza antibody subclass and effector functions from pandemic infection of children

  R

  •0•0•0•0•Updated Jan 30, 2024Jan 30, 2024

• SFLU_epitope_diveristy

  Public
  SFLU_epitope_diveristy

  R

  •0•0•0•0•Updated Jun 6, 2023Jun 6, 2023

• mutations-under-sarscov2-vaccination

  Public
  R

  •0•4•0•0•Updated Feb 23, 2023Feb 23, 2023

• SARS-CoV-2-sVNT-diversity

  Public
  R

  •0•0•0•0•Updated Oct 27, 2022Oct 27, 2022

• SynMut

  Public
  SynMut: An R Package for Designing Synonymously Mutated Sequences with Different Genomic Signatures

  R

  •2•0•0•0•Updated Jun 30, 2022Jun 30, 2022

• Barcoded-random-primer-sequencing

  Public
  R

  •0•0•0•0•Updated Jun 15, 2022Jun 15, 2022

• Vaccine-induced-selection-pressure-flu

  Public
  Vaccine induced selection pressure on seasonal influenza in mice

  R

  •0•2•0•0•Updated May 16, 2022May 16, 2022

• BA1_BA2_recombinant_HK

  Public
  Detection of a BA.1/BA.2 recombinant in Hong Kong, February 2022

  HTML

  •0•0•0•0•Updated Apr 1, 2022Apr 1, 2022

• BA.1-BA.2-competitive-transmission-hamster

  Public
  Analysis of NGS data from hamster samples

  HTML

  •0•0•0•0•Updated Mar 18, 2022Mar 18, 2022

• Parsing-SnpEff

  Public
  Use SnpEff to annotate SNPs and parse the results into table for regular uses.

  Python

  •1•7•0•0•Updated Feb 16, 2022Feb 16, 2022

• HK-Delta-variants

  Public
  Use of incoming travelers arriving at Hong Kong for genomic surveillance of SARS-CoV-2

  R

  •0•0•0•0•Updated Dec 20, 2021Dec 20, 2021

• Detection-of-B.1.1.529-variant-in-Hong-Kong

  Public
  Detection of SARS-CoV-2 B.1.1.529 variant in Hong Kong

  R

  •0•0•0•0•Updated Dec 20, 2021Dec 20, 2021

• VOC-SNPs-checking

  Public
  The repository hosts the R scripts for checking the number of lineage defining SNPs appeared in the input genomes.

  R

  •0•0•0•0•Updated Nov 27, 2021Nov 27, 2021

• Children-s-and-Adults-SARS-CoV-2-antibodies-responses

  Public
  Children's and Adults' SARS-CoV-2 antibodies responses

  R

  •0•0•0•0•Updated Nov 2, 2021Nov 2, 2021

• SNVs-comparison-table

  Public
  The scripts for generating SNVs comparision table on different samples basing on the variant calling results from iVar.

  HTML

  •0•0•0•0•Updated Sep 27, 2021Sep 27, 2021

• Check-primer-mismatch

  Public
  The scripts are used for detecting the level of SARS-CoV-2 primer/probe mismatches against the GISIAD database.

  R

  •0•1•0•0•Updated Jun 4, 2021Jun 4, 2021