Ilana and Pascal Mantoux Institute for Bioinformatics

Our Services

We support a wide range of bioinformatic and biostatistic analyses.

We can analyse data that originates from within the G-INCPM (NGS, proteomic and Drug Discovery), but can also analyse NGS data brought to us by the researcher, or published in public repositories.

We encourage the researchers to work closely with us and provide feedback and research questions, as we believe that this is important to gain biological insights from the data.

To start a project with us, click on the link below:

Start-a-project

Main applications:

 

RNA-seq

  • Quantification of gene expression levels
  • Differential expression
  • Differential splicing (exon usage)
  • Pathway enrichment (via a unique collaboration with GeneCards®)

ChIP-seq

 

  • Detection of binding sites for transcription factors, histone marks etc.
  • Differential binding analysis
  • Integration with RNA-seq data

Germline variant calling

  • Whole genome or whole exome
  • SNPs and Indels
  • Structural variants and copy number variation
  • Annotation of variants

Somatic variant calling

  • Whole genome or whole exome
  • Detection of SNPs and Indels
  • Annotation of variants
  • Estimation of clonality

Single cell RNA-seq

  • UMI-based (e.g. 10X Genomics) or whole transcript (e.g. SMARTseq2)
  • Clustering and visualization of cell populations
  • Differential gene expression

RRBS Bisulfite Methylation

 

  • Estimation of Methylation levels at a single nucleotide resolution

Bacterial genome assembly

  • Plasmid and genome sequences
  • Detection of structural variants and new genes
  • Can be combined with long reads to improve assembly quality

De novo transcriptome assembly

  • Novel transcripts
  • Quantification of expression levels
  • Annotation (via Blast2GO)
  • Can be combined with long reads to improve assembly quality

Custom applications

Can’t find you application here? We are open to new types of data and analysis

 

Output of a project:

The output of each project is an organized report, and all the accompanying raw and processed data.

An example report can be found here:

Example report: Re-analysis of published heart derived data-set