• Stars
    star
    1
  • Language
    R
  • Created over 6 years ago
  • Updated 8 months ago

Reviews

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

Repository Details

Pipelines for downloading and preparing TCGA data for analyses.

More Repositories

1

htsget-rs

A server implementation of the htsget protocol for bioinformatics in Rust
Rust
39
star
2

neoantigens

๐Ÿบ Exploring novel tumor epitope identification
Python
35
star
3

vcf_stuff

๐Ÿ“ŠEvaluating, filtering, comparing, and visualising VCF
Jupyter Notebook
26
star
4

umccrise

๐Ÿ DRAGEN Tumor/Normal workflow post-processing
Python
21
star
5

MAF-summary

Summary of a single or multiple MAF files.
R
10
star
6

infrastructure

Infrastructure as Code at UMCCR
Python
10
star
7

gpgr

๐Ÿ“š Genomics Platform Group Reporter
R
8
star
8

cwl-ica

A collection of cwl-ica workflows along with a user guide for the commands to use and contributions guide
Common Workflow Language
8
star
9

driver-analysis

Workflow for driver events identification across cohorts of tumours
R
7
star
10

RNAsum

Pipeline for generating RNAseq-based cancer patient reports
R
7
star
11

libica

๐Ÿ Python SDK for Illumina Connected Analytics (ICA) ๐Ÿ‰
Python
6
star
12

CNV_SV-visualisation

Visualise copy-number alterations and structural variants
R
5
star
13

sigrap

๐ŸŽถ Wrappers for somatic mutation signature analysis tools
R
5
star
14

umccr-dictionary

UMCCR Data Dictionary
Python
5
star
15

s3-rust-noodles-bam

Rust+AWS+S3+Lambda+Noodles = Serverless Bioinformatics
Rust
5
star
16

gridss-purple-linx-nf

Nextflow pipeline and AWS stack for the GRIDSS/PURPLE/LINX toolkit
Python
4
star
17

v2-samplesheet-maker

Generate V2 SampleSheets from JSON Inputs
Python
4
star
18

10x

๐Ÿš€ 10X dumping ground
HTML
4
star
19

TCGA-data-harmonization

Summary of TCGA datasets and steps for their harmonization.
4
star
20

sbeacon-exploration

Serverless Beacon v2 exploration for UMCCR use cases
Jupyter Notebook
4
star
21

orcabus

ย ๐Ÿ‹ UMCCR Pipeline & Workflow Orchestration
Python
4
star
22

illumination

๐Ÿ”† Interacting with Illumina Connected Analytics (ICA) API
EJS
3
star
23

holmes

BAM fingerprint stack
TypeScript
3
star
24

docker-who

A miscellaneous set of UMCCR dockerfiles that don't quite go anywhere else.
Dockerfile
3
star
25

elsa-data

Genomic data sharing support software ("let the data go")
TypeScript
3
star
26

RNA-seq-analysis

HTML
3
star
27

aws-benchmarks

Benchmarking different AWS Rust (vs non-Rust) client implementations
Rust
3
star
28

wrapica

A suite of secondary / tertiary functions for running ICA API calls
Python
2
star
29

beacon-doc

UMCCR Beacon Documentation
Jupyter Notebook
2
star
30

workflows

UMCCR production workflows
HTML
2
star
31

gen3-doc

UMCCR Gen3 Documentation
R
2
star
32

holmes-tools

Some python/bash tools that can be used against the Holmes fingerprint database to help investigations
Python
2
star
33

icav2-cli-plugins

A set of additional subcommands for icav2
Python
2
star
34

reference_data

Reference data version tracking for UMCCR
Python
1
star
35

oncoanalyser

Nextflow
1
star
36

g3po

๐Ÿค– Assorted utility CLI to work with Gen3
Python
1
star
37

data-portal-client

UMCCR Data Portal Frontend
TypeScript
1
star
38

data-portal-apis

UMCCR Data Portal API Backend in cloud native serverless
Python
1
star
39

aws_parallel_cluster

AWS Parallel Cluster setup for UMCCR
Shell
1
star
40

hmftools-nf

A comprehensive cancer WGS/WTS analysis and reporting pipeline from the Hartwig Medical Foundation
Nextflow
1
star
41

bcl2fastq-docker

1
star
42

illumination-v2

TypeScript
1
star
43

linxreport

Linx Result Reporter
R
1
star
44

BioSerDe

Bioinformatics format (De)Serialization
Rust
1
star
45

bcbio-varcall-doc

Documentation for bcbio somatic variant calling
Shell
1
star
46

fake-passport-ecosystem

A fake GA4GH passport ecosystem that can be deployed to AWS, or run locally
TypeScript
1
star
47

google_lims

Parsing Google-LIMS for dashboards and bcbio config files
HTML
1
star
48

cwl-ica-cli

The CLI used for creating/syncing CWL workflows from GitHub to ICAv1
Python
1
star