Pinned Repositories
Bulk_RNAseq
Bulk RNA-seq & Differential Gene Expression Analysis Workshop Material
mgikit
mgikit is a collection of tools used to demultiplex fastq files and generate demultiplexing and quality reports.
modules
Module files for Nextflow workflows
monolithic_bash_script_to_snakemake
nextflow-example-workflow-2024
A complete example workflow for the 2024 nextflow-vs-snakemake workshop (https://github.com/sagc-bioinformatics/nextflow-vs-snakemake-2024)
nextflow-vs-snakemake-2024
A homepage for our 2024 bioinformatics workflow managers workshop.
nf-rnaseq-sagc
RNAseq quantification pipeline
SAGC_5mCMethylation_tutorial
WGBS tutorial
spatial-workshop-may9
workshop-agrigenomics
SAGC - Bioinformatics's Repositories
sagc-bioinformatics/mgikit
mgikit is a collection of tools used to demultiplex fastq files and generate demultiplexing and quality reports.
sagc-bioinformatics/modules
Module files for Nextflow workflows
sagc-bioinformatics/nextflow-example-workflow-2024
A complete example workflow for the 2024 nextflow-vs-snakemake workshop (https://github.com/sagc-bioinformatics/nextflow-vs-snakemake-2024)
sagc-bioinformatics/nextflow-vs-snakemake-2024
A homepage for our 2024 bioinformatics workflow managers workshop.
sagc-bioinformatics/SAGC_5mCMethylation_tutorial
WGBS tutorial
sagc-bioinformatics/Bulk_RNAseq
Bulk RNA-seq & Differential Gene Expression Analysis Workshop Material
sagc-bioinformatics/monolithic_bash_script_to_snakemake
sagc-bioinformatics/nf-rnaseq-sagc
RNAseq quantification pipeline
sagc-bioinformatics/spatial-workshop-may9
sagc-bioinformatics/configs
Config files used to define parameters specific to compute environments at different Institutions
sagc-bioinformatics/demultiplex
Demultiplexing pipeline for sequencing data
sagc-bioinformatics/filesender-mp
Adapting filesender for SAGC use, adding functionalities
sagc-bioinformatics/mgikit-multiqc
MultiQC plugin to parse and integrate reports generated by mgikit demultiplexer
sagc-bioinformatics/nf-BCR-ABL1-breakpoint
Workflow version of Chung's previous pipeline which uses samtools and factera (v1.4.4)
sagc-bioinformatics/sagc-bioinformatics.github.io
South Australian Genomics Centre
sagc-bioinformatics/snakemake_basic_template
A basic Snakemake template repo
sagc-bioinformatics/snakemake_profiles
sagc-bioinformatics/workshop-agrigenomics
sagc-bioinformatics/workshop-sysadmin
sagc-bioinformatics/2022-snakemake-workshop
Snakemake workshop materials for the SAGC metagenomics + Snakemake workshop
sagc-bioinformatics/adapter-checks
sagc-bioinformatics/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
sagc-bioinformatics/nectar-workshop-deployment
Nectar setup for 2024 nextflow vs snakemake workshop
sagc-bioinformatics/SAGC_scRNAseq_workshop
SAGC scRNAseq workshop
sagc-bioinformatics/streamlit-barcode-checker
sagc-bioinformatics/test-datasets
Test data to be used for automated testing with the nf-core pipelines