erasmusmc-bioinformatics Goto Github PK

amr-galaxy-workflows

Workflows for WMDI - By Astrid Heikema & EMC Bioinformatics Team

argalaxy-docker

Docker image that sets up a Galaxy with the Immune Repertoire and SHM pipelines.

argalaxy-immunerepertoire

Argalaxy Immune Repertoire pipeline

argalaxy_docker

argalaxy_docker_fork

ash-ki67

enhanced automated segmentation and adaptive step finding for Ki67 hotspot detection in adrenal cortical cancer

benchamrking

benchamrking-scripts

Code for figures

changeo-db-to-ig-indel

Script that creates valid Ig-Indel input from a Change-O DB and fastq file and runs Ig-Indel on it.

crossmap_galaxy_wrapper

crossmap_galaxy_wrapper

demultiplex

A simple script to demultiplex fastq/fasta files (seperate into seperate fastq/fasta files based on barcodes)

dl_covid19

doval

dovalapi

Library for doval methods

emc-neoantigen

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction

emc-thesis-template

LaTeX template with correct margins, etc for Erasmus MC

erasmusmc-bioinformatics.github.io

ErasmusMC Bioinformatics Landing Page

flaimapper

:honeybee: Fragment Location Annotation Identification Mapper

fuma

:dash::leopard: Fusion Matcher: Match predicted fusions according to chromosomal location or gene annotation(s)

fumar

The R wrapper for FuMa, depending on Chimera

galactus-nextcloud

galaxy

Data intensive science for everyone.

galaxy-courses

Galaxy course documents and templates

galaxy-mothur-toolset

All information pertaining to the Galaxy Mothur Toolkit (GMT) project

galaxy-tools

Galaxy tools, datatypes and visualizations

galaxytools

:microscope::books: Galaxy Tool wrappers

galaxytools-emc

Tool Shed repositories maintained and developed by the Erasmus University Medical Center, following best practices guidelines set out by the Intergalactic Utilities Commission https://wiki.galaxyproject.org/IUC

gbm_drug_response

hpv-em

HPV-EM is an HPV genotyping tool that utilizes an expectation maximization algorithm to identify the presence of HPV genotypes in a sample from RNA-seq data

ifuse

Fusion Gene Explorer Docker image