irinastl's Stars
cov-lineages/pango-designation
Repository for suggesting new lineages that should be added to the current scheme
freebayes/freebayes
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
cov-lineages/pangolin
Software package for assigning SARS-CoV-2 genome sequences to global lineages.
CDCgov/SARS-CoV-2_Sequencing
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
StaPH-B/docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
artic-network/artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
yatisht/usher
Ultrafast Sample Placement on Existing Trees
jodyphelan/TBProfiler
Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
andersen-lab/Freyja
Depth-weighted De-Mixing
ncbi/vadr
Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation
seandavi/GEOquery
The bridge between the NCBI Gene Expression Omnibus and Bioconductor
cov-lineages/pangoLEARN
Store of the trained model for pangolin to access.
CDCgov/datasets-sars-cov-2
Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
pha4ge/pipeline-resources
Bioinformatics Pipeline and Visualization resources
cov-lineages/constellations
theiagen/public_health_viral_genomics
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
cov-lineages/scorpio
serious constellations of reoccurring phylogenetically-independent origin
nextstrain/nextclade_data
Datasets for https://github.com/nextstrain/nextclade
jodyphelan/tbdb
Standard database for the TBProfiler tool
CDCgov/cdcgov.github.io
Portal site for all CDCgov projects, https://cdcgov.github.io
nmdp-bioinformatics/pipeline
Consensus assembly and allele interpretation pipeline.
theiagen/terra_utilities
jonessarae/microarray-analysis
Analysis of microarray data using R.
pathogen-genomics/usher-public-workflow
A Dockstore WDL Workflow that uses UShER to place your consensus.fasta sequences on the SARS-CoV-2 phylogeny
theiagen/theiagen_docker_builds
irinastl/Gene-Expression-Data-Analysis-and-Visualization-in-RStudio
R codes and presentation