Stars
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
Reconstruction of focal amplifications with long reads
Computing statistics for overlapping sets of intervals
AWS for Bioinformatics Researchers
A curated and opinionated list of resources for Chief Technology Officers, with the emphasis on startups
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023
Genomic coordinates of problematic genomic regions as GRanges
Website to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.
Aggregates the results from AmpliconSuite for upload to AmpliconRepository.org
Structural variation caller using third generation sequencing
Pull current and historical baseball statistics using Python (Statcast, Baseball Reference, FanGraphs)
Streamlit — A faster way to build and share data apps.
State-of-the-Art Deep Learning scripts organized by models - easy to train and deploy with reproducible accuracy and performance on enterprise-grade infrastructure.
genepattern / AmpliconSuite
Forked from edwin5588/paa_customWraps the AmpliconSuite-pipeline workflow to identify one or more connected genomic regions which have copy number amplifications.
Snakemake-based workflow for detecting structural variants in genomic data
Graphical Fragment Assembly (GFA) Format Specification
GavinHaLab / Griffin
Forked from adoebley/GriffinA flexible framework for nucleosome profiling of cell-free DNA
🧬 gget enables efficient querying of genomic reference databases
Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
Various algorithms for analysing genomics data
Toolset for SV simulation, comparison and filtering