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    72 repositories

    • jvarkit-gradle

      Public
      Java utilities for Bioinformatics
      Java
      •
      Other
      •133•0•0•0•Updated Sep 18, 2024Sep 18, 2024

    • nf-core-modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •696•0•0•0•Updated Jun 11, 2024Jun 11, 2024

    • multi-package-containers

      Public
      Testing building mulled containers for multi-requirement tools.
      220•0•0•0•Updated Apr 20, 2024Apr 20, 2024

    • bcbio_docker

      Public
      Automated Docker builds for bcbio
      Dockerfile
      •
      MIT License
      •4•0•0•0•Updated Mar 23, 2024Mar 23, 2024

    • wf-human-variation

      Public
      Nextflow
      •
      Other
      •43•0•0•0•Updated Mar 19, 2024Mar 19, 2024

    • wf-basecalling

      Public
      Nextflow
      •
      Other
      •13•0•0•0•Updated Mar 19, 2024Mar 19, 2024

    • cnvkit-public

      Public
      Copy number variant detection from targeted DNA sequencing
      Python
      •
      Other
      •165•0•0•0•Updated Mar 1, 2024Mar 1, 2024

    • transcript-info

      Public
      Summary of RefSeq transcript alignment issues with human reference genomes (hg19, hg38)
      bioinformaticsalignmenttranscriptionhuman-genetics
      Apache License 2.0
      •0•0•0•0•Updated Jan 10, 2024Jan 10, 2024

    • nanoseq

      Public
      Nanopore demultiplexing, QC and alignment pipeline
      Nextflow
      •
      MIT License
      •79•0•0•0•Updated Nov 29, 2023Nov 29, 2023

    • paraphase

      Public
      HiFi-based caller for highly homologous genes
      Python
      •
      BSD 3-Clause Clear License
      •4•0•0•0•Updated Nov 9, 2023Nov 9, 2023

    • WisecondorX

      Public
      WisecondorX — An evolved WISECONDOR
      Python
      •
      Other
      •65•0•0•0•Updated Jun 28, 2023Jun 28, 2023

    • pgsc_calc

      Public
      The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation
      Nextflow
      •
      Apache License 2.0
      •21•0•0•0•Updated Apr 19, 2023Apr 19, 2023

    • varsim

      Public
      VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
      Java
      •
      BSD 2-Clause "Simplified" License
      •31•0•0•0•Updated Apr 7, 2023Apr 7, 2023

    • pgscatalog_utils

      Public
      Utilities for working with PGS Catalog API and scoring files
      Python
      •
      Apache License 2.0
      •3•0•0•0•Updated Mar 31, 2023Mar 31, 2023

    • HowTo_Calculation_PRS_CanRisk

      Public
      SOP for PRS calculation using CanRisk
      MIT License
      •2•0•0•0•Updated Mar 14, 2023Mar 14, 2023

    • cloudbiolinux

      Public
      CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
      Python
      •
      MIT License
      •158•0•0•0•Updated Nov 4, 2021Nov 4, 2021

    • ChromosomeMappings

      Public
      This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
      MIT License
      •59•0•0•0•Updated Sep 20, 2021Sep 20, 2021

    • iem

      Public
      Configuration files for the Illumina Experiment Manager
      bioinformaticsilluminaconfiguration-filesiem
      Apache License 2.0
      •0•1•0•0•Updated Aug 1, 2021Aug 1, 2021

    • black

      Public
      The uncompromising Python code formatter
      Python
      •
      MIT License
      •2.4k•0•0•0•Updated Jul 5, 2021Jul 5, 2021

    • jannovar

      Public
      Java library for annotating VCF files with gene/transcript-based annotations
      Java
      •
      Other
      •35•0•0•0•Updated Jun 6, 2021Jun 6, 2021

    • plantuml-visualizer

      Public
      🏭 A Chrome / Firefox extension for visualizing PlantUML code.
      TypeScript
      •
      Apache License 2.0
      •33•1•0•0•Updated Jan 24, 2021Jan 24, 2021

    • VEP_plugins

      Public
      Plugins for the Ensembl Variant Effect Predictor (VEP)
      Perl
      •
      Apache License 2.0
      •115•0•0•0•Updated Jul 3, 2020Jul 3, 2020

    • mosdepth

      Public
      fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
      Nim
      •
      MIT License
      •100•0•0•0•Updated Jun 23, 2020Jun 23, 2020

    • bcbio-nextgen-1

      Public
      Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
      Python
      •
      MIT License
      •354•0•0•0•Updated May 8, 2020May 8, 2020

    • Dark_and_Camouflaged_genes

      Public
      Shell
      •7•1•0•0•Updated Mar 11, 2020Mar 11, 2020

    • C4-PlantUML

      Public
      C4-PlantUML combines the benefits of PlantUML and the C4 model for providing a simple way of describing and communicate software architectures
      MIT License
      •1.1k•0•0•0•Updated Oct 26, 2019Oct 26, 2019

    • PharmCAT

      Public
      The Pharmacogenomic Clinical Annotation Tool
      Java
      •
      Mozilla Public License 2.0
      •39•0•0•0•Updated Aug 15, 2019Aug 15, 2019

    • hgvs

      Public
      Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
      Python
      •
      Apache License 2.0
      •94•0•0•0•Updated Jun 27, 2019Jun 27, 2019

    • CheatSheetSeries

      Public
      The OWASP Cheat Sheet Series was created to provide a concise collection of high value information on specific application security topics.
      Python
      •
      Other
      •3.9k•0•0•0•Updated May 6, 2019May 6, 2019

    • gatk-1

      Public
      Official code repository for GATK versions 4 and up
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •588•0•0•0•Updated Jan 25, 2019Jan 25, 2019