Repositories list

• CovRecomb

  Public
  A method to detect the inter-lineage recombinant of SARS-CoV-2

  Jupyter Notebook

  •0•1•0•0•Updated Sep 14, 2024Sep 14, 2024

• scImmuCC

  Public
  Hierarchical annotation of immune cells n scRNA-Seq data based on ssGSEA algorithm.

  R

  •2•6•5•0•Updated May 31, 2024May 31, 2024

• covSampler

  Public
  A subsampling method for large-scale SARS-CoV-2 genome data sets

  subsamplingsars-cov-2

  Python

  •

  MIT License

  •0•2•0•0•Updated Oct 3, 2023Oct 3, 2023

• sarscov2-omicron-nyc

  Public
  Early Introduction and Community Transmission of SARS-CoV-2 Omicron Variant, New York, New York, USA

  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Aug 1, 2023Aug 1, 2023

• estimate-bottleneck-size

  Public
  0•0•0•0•Updated Jul 24, 2023Jul 24, 2023

• CovRecomb_Simulation_Test

  Public
  The simulation test for the CovRecomb method using SARS-CoV-2 datasets.

  Python

  •

  MIT License

  •0•0•0•0•Updated May 4, 2023May 4, 2023

• SARS-CoV-2_webhub

  Public
  Website for SARS-CoV-2 genome evolution research

  JavaScript

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 30, 2022Nov 30, 2022

• sitePath_exec

  Public
  Command line executable for sitePath

  R

  •

  MIT License

  •0•0•0•0•Updated Nov 30, 2022Nov 30, 2022

• SARS-CoV-2_co-infection

  Public
  A computational method to identify the compositional lineage(s) in SARS-CoV-2 infected samples

  Python

  •

  MIT License

  •0•1•0•0•Updated Oct 5, 2022Oct 5, 2022

• sitePath

  Public
  Phylogenetic pathway–dependent recognition of fixed substitutions and parallel mutations

  mutationphylogenetics

  R

  •

  MIT License

  •2•8•4•0•Updated Sep 26, 2022Sep 26, 2022

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.3k•0•0•0•Updated Sep 23, 2022Sep 23, 2022

• SARS-CoV-2_paraFix

  Public
  SARS-CoV-2 paraFix mutations

  mutationssars-cov-2

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Sep 23, 2022Sep 23, 2022

• sitePath_assessment

  Public
  Test sitePath

  mutations

  R

  •0•1•0•0•Updated Sep 22, 2022Sep 22, 2022

• genome_treatment

  Public
  Some tools to treat aligned genome sequence.

  virus

  R

  •0•0•1•0•Updated Jun 30, 2022Jun 30, 2022

• sra2variant

  Public
  The pipeline to replace our CLC workbench

  Python

  •

  MIT License

  •2•0•0•0•Updated Apr 11, 2022Apr 11, 2022

• ImmuCC

  Public
  Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.

  gene-expressiondeconvolutionimmunoinformatics+ 1signature-genes

  R

  •23•23•6•0•Updated Nov 2, 2021Nov 2, 2021

• SARS-CoV-2_one_year

  Public
  Source code for the commentary paper

  mutationssars-cov-2

  Jupyter Notebook

  •0•0•0•0•Updated Feb 6, 2021Feb 6, 2021

• virome_pipeline

  Public
  A general pipeline constructed for viral metagenomes analysis from NGS read data.

  mosquitoviral-metagenomes-analysisvirome-pipeline

  R

  •

  MIT License

  •1•9•0•0•Updated Sep 3, 2020Sep 3, 2020

• RECDS

  Public
  RECDS identifies cluster-transition determining sites underlying the antigenic evolution of seasonal influenza viruses

  machine-learninginfluenzaantigenic-site

  Python

  •1•3•0•0•Updated Sep 3, 2020Sep 3, 2020

• CoroAnnoter

  Public
  A semi-automatic coronavirus genome annotation tool

  annotationgenomeblast+ 1coronavirus-genome

  R

  •0•0•0•0•Updated Jul 6, 2020Jul 6, 2020

• SARS-CoV-2_early_outbreak

  Public
  SARS-CoV-2 early outbreak analysis. Two polymorphism sites 8517 and 27641 (CDS numbering) were found to genotype the early strains.

  phylogeneticssnp-genotyping

  Jupyter Notebook

  •0•0•0•0•Updated Feb 28, 2020Feb 28, 2020