Bioinformatics Unit, Core Facility
We are the Bioinformatics Unit at the Core Facility at the Faculty of Medicine and Health Sciences. At present, we are located at the Hus 462, Floor 10.
About our services
RNAseq / Transcriptomics
- Bulk RNA sequencing analysis
- Single-cell RNA-seq analysis
- Allele-specific expression
- Long non-coding RNA expression
- Alternate splicing & Fusion genes
- Novel transcripts detection
- Microarray Data Analysis
Epigenomics
- DNA methylation Illimina Array Data Analysis - 450K, 850K (EPICv1), 935K (EPICv2)
- Short-read sequencing: Bisulfite sequencing (BS-seq) / Reduced Representation Bisulfite Sequencing (RRBS)
- Long-read sequencing: Nanopore and PacBio DNA methylation data analyses
- Enzymatic Methyl-seq: Twist Bioscience DNA methylation data analyses
Microbial and Viral
- Whole Genome (Short & Long read)
- 16S amplicon sequencing analysis
- Whole Metagenomic analysis
- Pan-genome analysis
- Viral metagenomics
- De-novo assembly & Annotation
- Mapping & Variant calling
Planning and Stats
- Project planning & consultation
- Pipeline Development
- Statistical calculations (R, SPSS)
- In-depth project discussions
Functional Analysis
- Ontology & Pathways
- Network analysis
- iPathwayGuide (Licensed)
- Interaction network analysis
Licensed Software
iPathwayGuide
Advanced analysis for GO, biological pathways, miRNA analysis, Disease networks, meta-analysis and interaction networks.
Pricing and collaboration
Initial Consultation
First meeting (up to 1 hour) is free for LiU and RÖ researchers.
Book Service
Long-term Project Support
Project data can be stored in our Nimbus storage for up to one year.
To accommodate publication timelines, extended storage of up to three years is available for LiU researchers, while external collaborators are supported for up to one year.
To accommodate publication timelines, extended storage of up to three years is available for LiU researchers, while external collaborators are supported for up to one year.
Web applications
Developed by Bioinformatics Core Facility, LiU. Hosted on SciLifeLab serve data center.
methyIR
A single shiny solution from sequencer data to pathway analysis. MethyIR is a comprehensive tool designed to streamline the analysis of methylation data from Illumia Methylation Arrays, providing an end-to-end solution from raw sequencing data to pathway analysis.
olinkwrapper
OlinkWrapper provides a user-friendly interface for performing quick analysis of Olink data using OlinkAnalyze package. It allows for data upload, parameter customization, visualization of results, and exporting of analysis outputs.
ShinyWGCNA
This Shiny app provides a user-friendly interface for performing Weighted Gene Co-expression Network Analysis (WGCNA) on RNA-seq/Microarray and DNA methylation (Array/Sequencing) data.
DataScanR
Data exploration analysis tool. Load your csv data file and it will help to clean the data, report the missing/NA values (using pareto graph), and perform varius statistical analyses resulting in tables and graphs.
gsalit
gsalit is a user-friendly Streamlit application that allows researchers to run the Illumina GSA (Global Screening Array) genotyping pipeline without manually handling command-line tools.
Infrastructure
Nimbus
Bioinformatics Core Facility primary storage server for research data at LiU. Maintained and supported by LiU-IT.
- Total Storage: >200TB
- Transfer Speed: 100 Mbps
- Backup: Periodically
Fraka
Bioinformatics Core Facility compute server for research data at LiU. Maintained and supported by LiU-IT.
- RAM: 2 TB
- Processor: 2 x 64 cores (256 threads) Intel Xeon Platinum 8592 + 3.9 GHz
- Network: 25 GBPS
- GPUs: 3x NVIDIA L40S 48 GB GDDR6
Compute Server
Nautilus
Bioinformatics Core Facility development server for research data at LiU.
- CPU: 2x 48 core Intel Xeon Gold
- RAM: 512 GiB DDR4
- GPUs: 2x dedicated NVIDIA GPUs
- Network: 1 GBPS transfer
Development Server
Contact us
Github Repositories: Open Access
Clinical Genomics, Sweden
We are also working with Clinical Genomics, Sweden from other Universities in Sweden to develop and integrate new analytic computational pipelines for big data analysis. Please find more details here: