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ER-User Guides

  • All content
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  • Training and Workshops
    • 2025 - eResearch Hands-On Training Workshops
    • 2024
      • Introduction to R
      • 2024 - Semester One: Hands-on variant calling and metagenomics analyses using QUT's HPC and Nextflow
      • 2024 - Semester Two: Hands on training workshops - HPC and Gene Expression (RNAseq and small RNAseq) analyses
        • 2024-2 eResearch - Session 2: Intro to HPC
        • 2024-S2 eResearch - Session 3: Introduction to Nextflow
          • 1. Getting started with Nextflow
          • 2. Nextflow pipeline repositories
          • 3. Running pipelines
          • 4. Input specifications
          • 5. Parameters
          • 6. Nextflow caching
          • 7. Nextflow pipeline outputs
          • 8. Where to from now?
        • 2024 eResearch - Session 4: nf-core-RNAseq pipeline
        • 2024-2 eResearch - Session 5: Differential expression analysis using R for RNAseq
        • 2024 eResearch - Session 6 : Small RNAs: A regulatory network of a broad range of biological processes
        • 2024-2 eResearch - Session 7: DE using R for smRNAseq
    • 2023
  • Start using the HPC
  • eResearch - single cell RNA-Seq analysis (10x Genomics)
  • eResearch - writing Nextflow workflows, beginner's guide
  • 2024 eResearch - Session 6 - Hands-on smRNAseq training
  • Data Download
  • 25S1W1 - legacy info
  • NextFlow quick start
  • nf-core/rnaseq - Gene Expression Analysis
  • nf-core/smrnaseq - Small RNA seq Analysis
  • nf-core/sarek - variant calling pipeline
  • nf-core/bactmap: A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
  • nf-epi2me-labs/wf-transcriptomes
  • nf-eresearch/ONTprocessing - NextFlow pipeline for Oxford Nanopore de novo assembly and ref guided consensus
  • nf-eresearch/ConsGenome: Nextflow based Genome Assembly, Variant Calling and building a Consensus Genome workflow
  • nf-eresearch/VirReport - Diagnosis of plant viruses and viroids using small RNA-seq data
  • nf-core/hic: Analysis of Chromosome Conformation Capture data (Hi-C)
  • nf-core/ampliseq 16S amplicon analysis pipeline (NextFlow Ampliseq)
  • nf-core/scrnaseq: A single-cell RNAseq pipeline for 10X genomics data
  • DESeq2 - Differential expression analysis
  • PacBio SMRT full length 16S analysis
  • PacBio SMRT command line Iso-seq analysis
  • ONT de novo genome assembly
  • ONT Oxford Nanopore fast5 processing
  • Variant filtering - screening homozygous recessive mutations
  • Anacapa - eDNA analysis toolkit
  • Automatic Assembly For The Fungi (AAFTF) pipeline
  • Extracting unmapped sequences
  • primalscheme - designing primer panels for multiplex PCR
  • draw.io Diagrams
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