Data Analysis for Molecular Biology Assays

 
Functionally Driven Molecular Profiling

  • Integration of functional results together with molecular profiling data and patients’ sample clinical information

 
Pharmacological Effects from Ex Vivo Assays

  • Curated pipelines supporting DNA-seq and RNA-seq methods. Standard and single cell approaches
  • First line analysis
  • DNA-Pipeline
  • QC analysis
  • Read filtering
  • Read mapping
  • Variant and InDels calling (with/without germline fraction)
  • Variant and Indels annotation and priorization
  • Copy Number variation identification (with/without germline fraction) and annotation
  • Other structural variation detection (subject to experimental design)
  • RNA Pipeline
  • QC analysis (Sequencing quality check + contamination check)
  • Read filtering
  • Read mapping
  • Detection of gene and transcript abundance
  • Differential gene expression
  • Gene set enrichment analysis (GSEA) of gene signatures that can represent molecular pathways, oncogenic signatures, immunologic signatures, GO terms, transcription factors, etc).
  • Downstream analysis