• Stars
    star
    1
  • Language
    Python
  • Created about 8 years ago
  • Updated almost 2 years ago

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

LIMS interface for the specific usage at Clinical Genomics

More 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

varg

variant validation report generator
Python
1
star
28

orderportal

Clinical genomics web interface for placing orders
1
star
29

versioning

Scripts and modules to automate versioning
Shell
1
star
30

hermes

Communication layer between CG and the pipelines.
Python
1
star
31

Metoid

Pipeline for metagenomic organism identification
Python
1
star
32

cgp-preparation-for-swedac-audit-2020

Preparation for Swedac audit 2020-06-10
1
star
33

shipping

Tool for deploying software
Python
1
star
34

statina

Python
1
star
35

databases

Scripts for interfacing with databases, SQL snippets, and schema overviews.
Python
1
star
36

reference-files

Small reference files
Lua
1
star
37

cgbeacon

Instructions and files to set up an Elixir-based beacon connected to a MySQL database.
Python
1
star
38

snippets

Code snippets and one liners
Shell
1
star
39

binaries

1
star
40

maintenance

Scripts for surveillance and monitoring, (backup), and general maintenance of data.
Shell
1
star
41

clinstatweb

Frontend overview webpages
JavaScript
1
star
42

cancerpipeline

Scripts handling our canceer pipeline
Shell
1
star
43

deliver

Scripts for automating data delivery and report generation of sequencing results
Python
1
star
44

genotype-ui

User interface for Genotype
CSS
1
star