Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
Projects in Awesome Lists by Clinical-Genomics
A curated list of projects in awesome lists by Clinical-Genomics .
https://github.com/clinical-genomics/genmod
Annotate models of genetic inheritance patterns in variant files (vcf files)
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/balsamic
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
bioinformatics genomics snakemake-workflows somatic-mutations variant-calling
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/mip
Mutation Identification Pipeline. Read the latest documentation:
analysis clinical pipeline variants
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/stranger
Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat
bioinformatics long-read long-read-sequencing massively-parallel-sequencing short-tandem-repeats
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/fusion-report
Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.github.io/fusion-report/example/
fusion-genes report visualization
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/patientmatcher
A MatchMaker Exchange server
diagnosis gene hpo-similarity matching-algorithm matchmaker matchmaking matchmaking-server omim patient-matching patients score similarity-score variants
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/loqusdb
A simple observation count database
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/downsampling
Downsample fastq files in an automated way
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/genotype
Simple genotype comparison of VCF files
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/cg
Glue between Clinical Genomics apps
Last synced: 03 Dec 2024
https://github.com/clinical-genomics/trailblazer
Keep track of and manage analyses
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/demultiplexing
To keep scripts associated with execution of the Illumina demultiplexing pipeline
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/build-podman
Build Podman with Github actions
build github-actions hpc-cluster podman
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/meatballs
An open source recipe book from the awesome staff of Clinical Genomics
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/loqusdbapi
A simple REST api for loqusdb
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/microsalt
Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
clinical microbial pipeline resistance typing
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/chanjo2
Persistent coverage analysis tool using the d4 format
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/mutacc
Mutation accumulation in a genomic background of reference samples
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/metoid
Pipeline for metagenomic organism identification
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/preclinvar
A ClinVar API submission helper written in FastAPI
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/crunchy
Compress fastq files with spring and check the integrity
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/saismatters
Fetal fraction estimation through fragment lenght profiling
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/varg
variant validation report generator
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/orderportal
Clinical genomics web interface for placing orders
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/cglims
LIMS interface for the specific usage at Clinical Genomics
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/hermes
Communication layer between CG and the pipelines.
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/salty-reporter
A tool to convert JASEN analysis result files in JSON format to the same format as the microSALT reports. Initially used to figure out discrepancies between the tools.
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/cgbeacon2
An updated beacon supporting GA4GH API 1.0
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/scout-reviewer-service
A rest service for generating REViewer output.
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/paneldb
A simple app to handle gene panels
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/primer-schemes
Primer schemes used by Clinical Genomics Stockholm
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/mongo_adapter
A python interface to handle connection to a mongod instance
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/limsmock
File-based mock for the lims REST API. For testing.
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/assets
A repo which contains assets such as images
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/cgface
Python package to connect to the cg REST API
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/mutant
Microbial Utility Toolbox And wrapper for data traNsmission and Transformation
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/.github
Default community health files
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/schug
All you need to know about genes, transcripts and exons
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/streamline-delivery
Project tracking for streamline-delivery
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/sendmail-container
Containerized mailing service
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/docker-base-images
A collection of useful images to be used as base images for Dockerfiles
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/mutacc-auto
Scripts to run mutacc import functionality automatically
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/cgstats
Models and connecting to clinstatsdb
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/dagger
A fast and quick way to build, visualize, and interact with dependency tree
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/janus
Repository to collect, parse and ship of multiqc data from housekeeper to cg.
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/event-driven-architecture
Project tracking for event driven POC
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/genotype-api
Rewrite of genotype package
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/cg-deployment
Clinical Genomics software deployment API
Last synced: 16 Dec 2024
https://github.com/clinical-genomics/bump2version-ci
Repository to host automated bump2version CI to run on python repositories
Last synced: 16 Dec 2024