Spaces
Apps
Templates
Create
ER-User Guides
All content
Space settings
Content
Results will update as you type.
Training and Workshops
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
•
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
•
Uploading sequence data to SRA
•
Copy of Copy of Hands-on smRNAseq training
•
Merging oligonucleotide sequences (local, HPC)
•
Bisulfite conversion WGBS
Equus caballus Project
•
Snakemake at QUT
ChIP-Seq
•
EBV genome integration data analysis
•
Common Nextflow errors
•
How to perform KEGG and GO enrichment analysis of non-model species (using R)
Legacy user guides
•
Using nf-core/sarek pipeline should be easy
bk_2024 - Semester One: Hands-on variant calling and metagenomics analyses using QUT's HPC and Nextflow
•
nf-core/rnaseq: downstream analysis in R
•
Downloading data from BaseSpace
•
RNAseq - Star 2 pass approach (Ronin)
•
Metagenomics Software on Ronin Cloud
•
RNA-seq using RASflow: genome- or transcriptome-based analysis
•
Deprecated - ONT variant analysis
•
Microbiome Analysis Infrastructure Roadmap V1.1
•
Downstream analysis of NextFlow ampliseq output (16S amplicon analysis)
•
VSD-1.0 (Virus Surveillance and Diagnosis)
•
Variant (vcf) analysis using R in Jupyter
•
Remove
•
Remove also
•
Creating links to open Jupyter Notebooks in the Jupyter Hub
copy Session 3 - Variant analysis using Nanopore data
copy_Session 5: Analysis of amplicon sequencing results in R
•
Copy of eResearch - single cell RNA-Seq analysis (10x Genomics)
•
Copy of Nanostring DSP protein assay data QC, exploration, normalisation and analysis.
•
Testing RNAseq parameters
•
Deprecated - SRA using SRA Toolkit
•
Nanostring - Nanostring DSP protein assay data QC, exploration, normalisation and analysis.
Apps
draw.io Diagrams
You‘re viewing this with anonymous access, so some content might be blocked.
Close
ER-User Guides
/
Remove
Remove
Paul Whatmore (Deactivated)
Owned by
Paul Whatmore (Deactivated)
Last updated:
Jan 13, 2021
Loading data...
{"serverDuration": 44, "requestCorrelationId": "9a001be0feb3428897cb905513f43af6"}