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bioconda-recipes

Conda recipes for the bioconda channel.

coroannoter

A semi-automatic coronavirus genome annotation tool

covrecomb

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

covrecomb_simulation_test

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

covsampler

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

estimate-bottleneck-size

genome_treatment

Some tools to treat aligned genome sequence.

immucc

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

recds

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

sars-cov-2_co-infection

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

sars-cov-2_early_outbreak

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

sars-cov-2_one_year

Source code for the commentary paper

sars-cov-2_parafix

SARS-CoV-2 paraFix mutations

sars-cov-2_webhub

Website for SARS-CoV-2 genome evolution research

sarscov2-omicron-nyc

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

scimmucc

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

sitepath

Phylogenetic pathway–dependent recognition of fixed substitutions and parallel mutations

sitepath_assessment

Test sitePath

sitepath_exec

Command line executable for sitePath

sra2variant

The pipeline to replace our CLC workbench

virome_pipeline

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