What expertise can SBC offer?

The SBC has expertise in the following areas, and software packages. If you are interested in some software or methodologies not listed here, please ask.

Experimental Design

If you are planning an experiment, please come to us before generating data so that we can discuss the design…

The Core is experienced in advising on the following issues:-

Optimal number of replicates
Biases and confounding factors
Single-end or paired-end sequencing
Depth of sequencing required
Contacts at Sequencing vendors

SITraN multi-omics facility

Genomics Facility in Biosciences

Next Generation Sequencing (NGS) Analysis

Retrieval and analysis of public datasets on Gene Expression Omnibus (GEO) and Sequencing Read Archive (SRA)
BWA, and other aligners for all NGS platforms and applications
edgeR, DESeq2, STAR and salmon (among others) for RNA-Seq analysis and differential expression
Clustering and PCA to identify batch effects
Downstream analysis of gene lists to identify over-represented pathways / ontologies using GSEA, goseq, or other online tools such as DAVID
Alternative splicing analysis and visualization (e.g. sashimi plots)
GATK, VarScan and MuTect for somatic and germline mutation calling
MACS2, and other peak callers for ChIP-Seq and ATAC-seq analysis
Submission of data to public repositories for publication

Single Cell RNA-Seq

Running cellranger
QC of single-cell RNA-seq and filtering poor quality cells / samples
Dimensionality reduction and plotting with UMAP, TSNE etc
Marker gene identification
Analysis of Spatial transcriptomics data

Microarray Analysis

Experience with data from gene expression data from Affymetrix and Illumina platforms
Re-analysing public data deposited on GEO or ArrayExpress
Experience with varying data types, including expression, methylation (450K), SNP and copy-number

Further Expertise

Custom visualisation of high-throughput data
Implementing and running workflows and piplines with nextflow
Packaging and deploying software environments with docker
Data Management and curation
Creating interactive web applications wih Shiny

For queries relating to collaborating with the Bioinformatics Core team on projects: bioinformatics-core@sheffield.ac.uk

Join our mailing list so as to be notified when we advertise talks and workshops by subscribing to this Google Group. You can also connect with us on Linkedin.

Requests for a Bioinformatics support clinic can be made via the Research Software Engineering (RSE) code clinic system. This is monitored by Bioinformatics Core staff, so we will ensure the appropriate expertise (which may involve individuals from multiple teams) will be available to help you

Queries regarding sequencing and library preparation provision at The University of Sheffield should be directed to the Multi-omics facility in SITraN or the Genomics Laboratory in Biosciences.