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htsget-rs
A server implementation of the htsget protocol for bioinformatics in Rustneoantigens
๐บ Exploring novel tumor epitope identificationvcf_stuff
๐Evaluating, filtering, comparing, and visualising VCFumccrise
๐ DRAGEN Tumor/Normal workflow post-processingMAF-summary
Summary of a single or multiple MAF files.infrastructure
Infrastructure as Code at UMCCRgpgr
๐ Genomics Platform Group Reportercwl-ica
A collection of cwl-ica workflows along with a user guide for the commands to use and contributions guidedriver-analysis
Workflow for driver events identification across cohorts of tumourslibica
๐ Python SDK for Illumina Connected Analytics (ICA) ๐CNV_SV-visualisation
Visualise copy-number alterations and structural variantssigrap
๐ถ Wrappers for somatic mutation signature analysis toolsumccr-dictionary
UMCCR Data Dictionarys3-rust-noodles-bam
Rust+AWS+S3+Lambda+Noodles = Serverless Bioinformaticsgridss-purple-linx-nf
Nextflow pipeline and AWS stack for the GRIDSS/PURPLE/LINX toolkitv2-samplesheet-maker
Generate V2 SampleSheets from JSON Inputs10x
๐ 10X dumping groundTCGA-data-harmonization
Summary of TCGA datasets and steps for their harmonization.sbeacon-exploration
Serverless Beacon v2 exploration for UMCCR use casesorcabus
ย ๐ UMCCR Pipeline & Workflow Orchestrationillumination
๐ Interacting with Illumina Connected Analytics (ICA) APIholmes
BAM fingerprint stackdocker-who
A miscellaneous set of UMCCR dockerfiles that don't quite go anywhere else.elsa-data
Genomic data sharing support software ("let the data go")RNA-seq-analysis
aws-benchmarks
Benchmarking different AWS Rust (vs non-Rust) client implementationswrapica
A suite of secondary / tertiary functions for running ICA API callsbeacon-doc
UMCCR Beacon Documentationworkflows
UMCCR production workflowsgen3-doc
UMCCR Gen3 Documentationholmes-tools
Some python/bash tools that can be used against the Holmes fingerprint database to help investigationsicav2-cli-plugins
A set of additional subcommands for icav2reference_data
Reference data version tracking for UMCCRTCGA-data-prep
Pipelines for downloading and preparing TCGA data for analyses.oncoanalyser
g3po
๐ค Assorted utility CLI to work with Gen3data-portal-client
UMCCR Data Portal Frontenddata-portal-apis
UMCCR Data Portal API Backend in cloud native serverlessaws_parallel_cluster
AWS Parallel Cluster setup for UMCCRhmftools-nf
A comprehensive cancer WGS/WTS analysis and reporting pipeline from the Hartwig Medical Foundationbcl2fastq-docker
illumination-v2
linxreport
Linx Result ReporterBioSerDe
Bioinformatics format (De)Serializationbcbio-varcall-doc
Documentation for bcbio somatic variant callingfake-passport-ecosystem
A fake GA4GH passport ecosystem that can be deployed to AWS, or run locallygoogle_lims
Parsing Google-LIMS for dashboards and bcbio config filescwl-ica-cli
The CLI used for creating/syncing CWL workflows from GitHub to ICAv1Love Open Source and this site? Check out how you can help us