virology
There are 7 repositories under virology topic.
globalcitizen / 2019-wuhan-coronavirus-data
2019 Wuhan Coronavirus data (COVID-19 / 2019-nCoV)
Language:PHP 613- COVID-19-data
starschema / COVID-19-data
Unpivoted and cleaned data sets on the COVID-19 pandemic
Language:Jupyter Notebook 85 chanzuckerberg / czid-web
Infectious Disease Sequencing Platform
Language:TypeScript 77- BioExplorer
BlueBrain / BioExplorer
The Blue Brain BioExplorer (BBBE) is a tool for data visualization experts and scientists to extract and analyze scientific data from visualization and interactive exploration
Language:C++ 62 - Language:Shell 50
jaleezyy / covid-19-signal
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
Language:Python 30DennisSchmitz / Jovian_archive
Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.
Language:Python 18viromelab / tracespipe
Reconstruction and analysis of viral and host genomes at multi-organ level
Language:Shell 16- Language:Perl 14
- zoonotic_rank
Nardus / zoonotic_rank
Code and data used in Mollentze et al. (2021) "Identifying and prioritizing potential human-infecting viruses from their genome sequences".
Language:R 11 babinyurii / recan
genetic distance plotting for recombination events analysis
Language:Python 9RIVM-bioinformatics / SARS2seq
SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.
Language:Python 6TrueConsense is a consensus caller for viral-targets that create biologically correct consensus sequences. TrueConsense keeps track of open reading frames, compensates for common sequencing or alignment artefacts, and is able to generate consensus sequences on multiple coverage-thresholds at the same time
Language:Python 5- decouphage
voorloopnul / decouphage
The art of decorating a phage genome by gluing feature cutouts into it.
Language:Python 5 NGS data analysis scripts for HBV elimination research group
Language:Python 4ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome
Language:Python 4jvanheld / SARS-CoV-2_origins
Analysis of insertions in the genomes and proteins of coronaviruses. Illustration: AvH. (2020). Covid-19 cracked <http://doi.org/10.5281/zenodo.3734643>
Language:HTML 3- Language:Java 3
- Language:Python 2
- Language:JavaScript 2
athaun / cell-regen-influenza-model
An influenza virus model examining the effects of cellular regeneration on cell-to-cell and cell-free viral transmission.
Language:Python 2NGS data analysis scripts for HBV elimination research group
Language:Python 2workflow and notes on large virus genome assembly and snp call using FastQC, Trimmomatic, bowtie2, and samtools.
Language:HTML 2CorrieGunter / particle_counter
Circular particle counter for electron microscope images
Language:Jupyter Notebook 2jhuapl-bio / AGAVE
Automated Genomics Application for Variant Exploration (AGAVE)
Language:Vue 2- Bio-Virologia
AimerGDiaz / Bio-Virologia
Primer Bookdown de Virología en Español
Language:TeX 1 - Language:Ruby 1
gbwiersum / NUDataSciSummer2020
This is a project for Northwestern's CIS395 course in DataScience. This project implements a pipeline to determine genetic distance between all coronavirus genomes contained in the NIH Coronavirus dataset.
Language:Jupyter Notebook 1janieslab / SARS-CoV-2_VariantDashboard
Data and code related to the Janies Lab Variant Dashboard for SARS-CoV-2
Language:R 1kagningemma / sapovirus-evolution
These are scripts relevant to the study of sapovirus intrahost and interhost genome evolution. The scripts are relevant to (1) the mining of inter-genotype evolution, (2) within and between-host sapovirus genome evolutionary analyses, (3) sapovirus genetic divergence and diversity.
Language:Jupyter Notebook 1naturepoker / phaster_kits
Quality of life improvement scripts for working with https://phaster.ca (PHAge Search Tool Enhanced Release)
Language:Shell 1oleksulkowski / Syn-CpG-Spacer
A Panel progressive web app for synonymous recoding of viral genomes with CpG dinucleotides
Language:Python 1PoisotLab / ms_svd_imputation
Imputation of missing interactions using SVD
Language:TeX 1Rapid-Deployment-Vaccine-Collaborative / Gen-11
SARS-CoV-2 Peptide Vaccine, Gen 11
viralemergence / trefle
Imputing the mammalian virome with the LF-SVD model
Language:Julia 1
