Genomic Services

PROJECT DETAILS


Description

KCL & NIHR Maudsley BRC/U Precision Health Informatics Core Bioinformatics Service provides a wide range of bioinformatics solutions to fully support genomic-related research. The team specialises in comprehensive data analyses for in-house and external generated microarray and next generation sequencing (NGS) projects. We provide various levels of support including experimental design, data analyses, result interpretation and practical data management.
Services offered include:

  • Illumina Beadarray Pre-Processing
    • SNP: Raw IDAT to genotype calls (PLINK binary format)
    • Gene Expression: Raw IDAT to gene expression summaries (.RData expression set file and .txt files)
  • Affymetrix Gene Expression Array Pre-Processing
    • Raw data to gene expression summaries (.RData expression set file and .txt files)
  • GWAS
    • QC
    • Imputation
    • Polygenic Risk Score (PRS) calculation
    • Custom analyses
  • Gene Expression Array Analysis
    • Pre-processing and QC
    • Standard Differential Expression (DE) analysis (Limma or SAM)
    • Co-Expression Analysis (WGCNA)
    • Custom analyses
  • NGS DNA-Seq
    • QC (fastqc and read quality trimming)
    • Alignment (bwa and snap)
    • Variant calling (SNP, INDELS, CNV and ensemble SNV calls)
    • Variant annotation (Annovar, snpEFF and VEP)
    • GATK best practices pipeline (haplotype caller and gVCF)
    • bcbio-nextgen pipeline
    • NGS custom pipeline
  • NGS RNA-Seq
    • QC (fastqc and read quality trimming)
    • DE (Kalisto)
    • Cufflinks workflow
    • HISAT, StringTie and Ballgown
    • bcbio-nextgen pipeline
    • GATK Star pipeline
    • Custom pipeline
  • Somalogic data processing and analysis
  • RedCap database setup
  • GenomeStudio workstation use
  • Bioinformatics training
  • Custom scripting and analyses
  • Project design & grant writing

Our innovative, affordable, and reliable solutions are available in the form of “Full Collaboration”, basic “Collaboration” or a simple “fee-for-service”. In addition, our team offers a unique consultation service at any stage of a project. For further information, please contact hamel.patel@kcl.ac.uk

Genomics Services

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