Repositories list

• MtbImporter

  Public
  Fully automated data import tool for cBioPortal (https://github.com/cbioportal/cbioportal). Best deployed with MTB-cBioPortal (https://github.com/buschlab/MTB-cbioportal) and MIRACUM-Pipe (https://github.com/AG-Boerries/MIRACUM-Pipe-docker).

  Java

  •

  GNU Affero General Public License v3.0

  •0•3•1•3•Updated Nov 8, 2024Nov 8, 2024

• fhirspark

  Public
  Java

  •

  GNU Affero General Public License v3.0

  •3•0•1•1•Updated Nov 7, 2024Nov 7, 2024

• MtbExporter

  Public
  Java

  •

  GNU Affero General Public License v3.0

  •0•2•1•1•Updated Nov 7, 2024Nov 7, 2024

• MTB-cbioportal

  Public
  cBioPortal is a data visualization tool for cancer genomics. This repository contains all components to deploy the customized version of cBioPortal used in the PM4Onco use case of the Medical Informatics Initiative Germany.

  cbioportalfhirprecision-oncology+ 3medical-informatics-initiativemiracumpm4onco

  Shell

  •

  GNU Affero General Public License v3.0

  •6•7•2•3•Updated Nov 5, 2024Nov 5, 2024

• MMRd

  Public
  Predicting MMR status based on Albayrak et al. (2020)

  R

  •1•0•0•0•Updated Oct 30, 2024Oct 30, 2024

• cbioportal-frontend

  Public
  React Frontend of cBioPortal 🎉

  TypeScript

  •

  GNU Affero General Public License v3.0

  •271•0•0•1•Updated Oct 22, 2024Oct 22, 2024

• MIRACUM-Pipe

  Public
  Whole exome sequencing pipeline including advanced variant annotation features and automated PDF reporting.

  R

  •

  GNU Affero General Public License v3.0

  •14•0•0•0•Updated Oct 10, 2024Oct 10, 2024

• bam-matcher

  Public
  Python

  •

  Creative Commons Attribution 4.0 International

  •1•0•0•2•Updated Oct 8, 2024Oct 8, 2024

• cbioportal

  Public
  cBioPortal for Cancer Genomics

  Java

  •

  GNU Affero General Public License v3.0

  •505•0•0•0•Updated Apr 9, 2024Apr 9, 2024

• sequenza

  Public
  ❗ This is a read-only mirror of the CRAN R package repository. sequenza — Copy Number Estimation from Tumor Genome Sequencing Data. Homepage: https://sequenzatools.bitbucket.io, Mailing list: https://groups.google.com/forum/#!forum/sequenza-user-group Report bugs for this package: https://bitbucket.org/sequenzatools/sequenza/issues

  R

  •5•0•0•0•Updated Feb 6, 2024Feb 6, 2024

• cbioportal-core

  Public
  Legacy cBioPortal Core

  Java

  •15•0•0•0•Updated Feb 2, 2024Feb 2, 2024

• MIRACUM-Pipe-singularity

  Public
  MIRACUM-Pipe is a whole exome and panel sequencing pipeline for precision oncology (https://github.com/AG-Boerries/MIRACUM-Pipe). This repository is a port of the pipeline running inside a singularity container.

  omicsomics-pipelineprecision-oncology+ 4medical-informatics-initiativemiracumbioinformaticsngs

  R

  •

  GNU Affero General Public License v3.0

  •1•4•0•0•Updated Oct 24, 2023Oct 24, 2023

• copynumber

  Public
  R

  •0•0•0•0•Updated Oct 20, 2023Oct 20, 2023

• vep

  Public
  Recipe for VEP + Cache

  5•1•0•0•Updated Sep 29, 2023Sep 29, 2023

• HowTos

  Public
  Manuals and examples

  Python

  •1•2•0•0•Updated Sep 22, 2022Sep 22, 2022

• 2022_canine_atopic_dermatitis_paper

  Public
  R

  •1•1•0•0•Updated Jun 29, 2022Jun 29, 2022

• bamsnap

  Public
  HTML

  •

  MIT License

  •25•0•0•0•Updated Nov 24, 2021Nov 24, 2021

• NGS-tools-and-scripts

  Public
  R

  •2•0•0•0•Updated Jan 22, 2021Jan 22, 2021

• cbioportal-tools

  Public
  Perl

  •0•0•0•0•Updated Nov 19, 2020Nov 19, 2020

• TF_enrichment_analysis

  Public
  COVIDomics paper: Transcription factor activity network

  R

  •3•0•0•0•Updated Nov 13, 2020Nov 13, 2020

• Egyptref

  Public
  Scripts and pipelines used in the generation of "An Egyptian Genome Reference"

  Perl

  •1•1•0•0•Updated Jun 22, 2020Jun 22, 2020

• lied_egypt_genome

  Public
  Python

  •2•0•0•0•Updated Jun 19, 2020Jun 19, 2020

• 2020_population_genetics

  Public
  Python

  •2•0•0•0•Updated Jun 19, 2020Jun 19, 2020

• awesome-deepbio

  Public
  A curated list of awesome deep learning applications in the field of computational biology

  314•1•0•0•Updated Jul 30, 2018Jul 30, 2018

• NGS_tools

  Public
  Collection of tools for next generation sequencing analysis

  GNU General Public License v3.0

  •2•0•0•0•Updated May 29, 2018May 29, 2018

• usefulStuff

  Public
  Collection of useful links

  2•0•0•0•Updated Apr 11, 2018Apr 11, 2018