Pinned Repositories
variant_pipeline
Work on the variant_pipeline and initial r analysis used in calling variants from NGS data
CodonShuffle
JVI_Gem_2018
Known viral evolutionary rates, mutation rates, and genome sizes.
Host_level_IAV_evolution
COVID19SequenceCompile
SARSCov2_Intrahost
Repository to accompany our paper on SARS-CoV-2 intrahost genetic diversity.
sapphire_covid_display
Sample Shiny application code
Fluvacs_paper
Host_level_IBV_evolution
Repository for analysis of influenza B virus within and between hosts from the HIVE.
Flutes_within-host_evolution
Repository for data and code from the FluTES study on within-host evolution
Lauring Lab's Repositories
lauringlab/COVID19SequenceCompile
lauringlab/Flutes_within-host_evolution
Repository for data and code from the FluTES study on within-host evolution
lauringlab/.github
lauringlab/IVYIC_FINAL
lauringlab/SARS-CoV-2_VOC_transmission_bottleneck
lauringlab/shared_app_code_no_data
lauringlab/weightedMI
A package for computing weighted MI and entropy from multiple sequence alignments
lauringlab/timeMI
This is a package to calculate inverse weighted entropy and MI values for an MSA to account for uneven time sampling
lauringlab/SARS-CoV-2_Household_diversity
lauringlab/general_reports_sc2
lauringlab/sapphire_covid_display
Sample Shiny application code
lauringlab/sarscov2_application
fully integrated system for processing sars-cov2 genome sequences
lauringlab/AlertCode
Place to store code sets for sending alert + info messages to Slack channel #underworld
lauringlab/SARS2_Fall_2020
lauringlab/SARSCov2_Intrahost
Repository to accompany our paper on SARS-CoV-2 intrahost genetic diversity.
lauringlab/DonorDerivedInfection
lauringlab/IAV_within-host_Ne
Data and code used to model the within-host allele trajectories
lauringlab/ProlongedReplicationCase
lauringlab/Poliovirus_Intrahost
lauringlab/Host_level_IBV_evolution
Repository for analysis of influenza B virus within and between hosts from the HIVE.
lauringlab/NGS_mutation_rate_assay
This repository contains scripts that were used during my use of Illumina sequencing to determine mutation rates.
lauringlab/variant_pipeline
Work on the variant_pipeline and initial r analysis used in calling variants from NGS data
lauringlab/JVI_Gem_2018
Known viral evolutionary rates, mutation rates, and genome sizes.
lauringlab/Host_level_IAV_evolution
lauringlab/Host_level_IAV_app
A shiny app for exploring the iSNV in our data set especially those in transmission pairs
lauringlab/Host_level_influenza_app
A shiny app for exploring the iSNV in our data set especially those in transmission pairs
lauringlab/benchmarking_shiny
A shiny app that runs a summary of the benchmarking analysis. A smaller version is hosted on the website.
lauringlab/speed_fidelity
lauringlab/TsTv_paper
lauringlab/Fluvacs_paper