Clinical Genomics (@Clinical-Genomics)
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Clinical-Genomics

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Top repositories

1

scout

VCF visualization interface
HTML
149
star
2

genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)
Python
75
star
3

chanjo

Chanjo provides a better way to analyze coverage data in clinical sequencing.
Python
49
star
4

BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
Python
44
star
5

MIP

Mutation Identification Pipeline. Read the latest documentation:
Perl
42
star
6

stranger

Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat
Python
30
star
7

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/
Python
24
star
8

patientMatcher

A MatchMaker Exchange server
Python
11
star
9

downsampling

Downsample fastq files in an automated way
Shell
9
star
10

loqusdb

A simple observation count database
Python
9
star
11

genotype

Simple genotype comparison of VCF files
Python
8
star
12

demultiplexing

To keep scripts associated with execution of the Illumina demultiplexing pipeline
Python
5
star
13

cg

Glue between Clinical Genomics apps
Python
5
star
14

trailblazer

Keep track of and manage analyses
Python
5
star
15

build-podman

Build Podman with Github actions
Shell
4
star
16

cg_lims

Python
3
star
17

clinical

General python modules for e.g. database access
Python
2
star
18

SAISMATTERS

Fetal fraction estimation through fragment lenght profiling
Python
2
star
19

mutacc

Mutation accumulation in a genomic background of reference samples
Python
2
star
20

housekeeper

File data orchestrator
Python
2
star
21

meatballs

An open source recipe book from the awesome staff of Clinical Genomics
Python
2
star
22

loqusdbapi

A simple REST api for loqusdb
Python
2
star
23

preClinVar

A ClinVar API submission helper written in FastAPI
Python
2
star
24

microSALT

Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
Python
2
star
25

backup

Shell
2
star
26

chanjo2

Persistent coverage analysis tool using the d4 format
Python
2
star
27

cglims

LIMS interface for the specific usage at Clinical Genomics
Python
1
star
28

varg

variant validation report generator
Python
1
star
29

orderportal

Clinical genomics web interface for placing orders
1
star
30

versioning

Scripts and modules to automate versioning
Shell
1
star
31

hermes

Communication layer between CG and the pipelines.
Python
1
star
32

Metoid

Pipeline for metagenomic organism identification
Python
1
star
33

cgp-preparation-for-swedac-audit-2020

Preparation for Swedac audit 2020-06-10
1
star
34

shipping

Tool for deploying software
Python
1
star
35

statina

Python
1
star
36

databases

Scripts for interfacing with databases, SQL snippets, and schema overviews.
Python
1
star
37

reference-files

Small reference files
Lua
1
star
38

cgbeacon

Instructions and files to set up an Elixir-based beacon connected to a MySQL database.
Python
1
star
39

snippets

Code snippets and one liners
Shell
1
star
40

binaries

1
star
41

maintenance

Scripts for surveillance and monitoring, (backup), and general maintenance of data.
Shell
1
star
42

clinstatweb

Frontend overview webpages
JavaScript
1
star
43

cancerpipeline

Scripts handling our canceer pipeline
Shell
1
star
44

deliver

Scripts for automating data delivery and report generation of sequencing results
Python
1
star
45

genotype-ui

User interface for Genotype
CSS
1
star