Giters
Clinical Genomics (Clinical-Genomics)

Clinical Genomics

Clinical-Genomics

Geek Repo

Location:Stockholm, Sweden

Home Page:https://clinical.scilifelab.se/

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Clinical Genomics's repositories

scout

VCF visualization interface

Language:HTMLLicense:BSD-3-ClauseStargazers:144Issues:14Issues:2410

genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)

Language:PythonLicense:MITStargazers:70Issues:9Issues:90

chanjo

Chanjo provides a better way to analyze coverage data in clinical sequencing.

Language:PythonLicense:MITStargazers:48Issues:10Issues:175

BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Language:PythonLicense:MITStargazers:43Issues:10Issues:606

stranger

Tool to annotate outfiles from ExpansionHunter with the pathologic implications of the repeat

Language:PythonLicense:MITStargazers:27Issues:6Issues:25

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/

Language:PythonLicense:GPL-3.0Stargazers:24Issues:5Issues:42

loqusdb

A simple observation count database

Language:PythonLicense:MITStargazers:8Issues:5Issues:57

cg

Glue between Clinical Genomics apps

Language:PythonStargazers:6Issues:9Issues:986

raredisease

CG's rare disease pipeline in next flow, see the main repo here 👇

Language:NextflowLicense:MITStargazers:5Issues:4Issues:20

trailblazer

Keep track of and manage analyses

Language:PythonLicense:MITStargazers:5Issues:8Issues:97

cg_lims

Language:PythonStargazers:3Issues:7Issues:256

clinical_EPPs

EPPs used in clinical genomics LIMS

Language:PythonStargazers:3Issues:9Issues:91

chanjo2

Persistent coverage analysis tool using the d4 format

Language:PythonStargazers:2Issues:4Issues:125

housekeeper

File data orchestrator

Language:PythonLicense:MITStargazers:2Issues:0Issues:0

meatballs

An open source recipe book from the awesome staff of Clinical Genomics

Language:PythonLicense:MITStargazers:2Issues:3Issues:10

microSALT

Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.

Language:PythonLicense:GPL-3.0Stargazers:2Issues:9Issues:51

crunchy

Compress fastq files with spring and check the integrity

Language:PythonLicense:MITStargazers:1Issues:7Issues:6

gens

Language:JavaScriptLicense:MPL-2.0Stargazers:1Issues:3Issues:22

hermes

Communication layer between CG and the pipelines.

Language:PythonStargazers:1Issues:14Issues:15

preClinVar

A ClinVar API submission helper written in FastAPI

Language:PythonLicense:MITStargazers:1Issues:2Issues:44

genotype-api

Rewrite of genotype package

Language:PythonStargazers:0Issues:7Issues:45

MUTANT

Microbial Utility Toolbox And wrapper for data traNsmission and Transformation

Language:PythonLicense:GPL-3.0Stargazers:0Issues:9Issues:95

statina-ui

Frontend app for Statina

Language:TypeScriptStargazers:0Issues:7Issues:103

arnold

Language:PythonLicense:MITStargazers:0Issues:6Issues:18

chanjo-report

Report generator for Chanjo output

Language:PythonLicense:MITStargazers:0Issues:7Issues:22

event-driven-architecture

Project tracking for event driven POC

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flask-ldapconn

Flask extension providing python-ldap3 connection and ORM for accessing LDAP servers.

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Janus

Repository to collect, parse and ship of multiqc data from housekeeper to cg.

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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.

Language:HTMLLicense:GPL-3.0Stargazers:0Issues:0Issues:0

schug

All you need to know about genes, transcripts and exons

Language:PythonStargazers:0Issues:4Issues:25