Bioinformatics Support Platform for data analysis

header bioinformatics

 

The Bioinformatics Support Platform of the Faculty of Medicine provides consulting and assistance in data analysis. We organise permanencies twice a week, and can provide embedded bioinformatics support where we promote users training.

Check our services

Our Expertise

At the platform, we have experience in the following fields. More may be added depending on the requests of the faculty members.

 

Data science:
Data visualisation
R language + Bioconductor
Data managment (organize, archive, share)
Data submission (GEO, Yareta)
High Performance Computing (cluster Baobab)
Mathematical Modelisation
Machine Learning (including deep-learning with Keras)
Databases query
Data integration
Big Data File Handling (hdf5 format)
Data browsing web site (shiny)

Reproducible Science Tools:
GitLab Unige
Docker
Renku (under beta testing)

Programming Langages:
R, C/C++, BASH, Slurm, Python, Sun Grid


Operating Systems:

Linux, OSX, Windows


Other:
Illustrator
Support in writting DMP

Genomic Sequencing, including:
Whole Exome Sequencing
Whole Genome Sequencing
de novo assembly
Tn-Seq
ChIP-Seq
ChEC-Seq

Single-cell transcriptomics
RNA-Seq
Ribo-Seq
CRAC-Seq
PAR-CLIP
NET-Seq
RIP-Seq


Reads Aligners:
bwa, STAR, bowtie, bowtie2, hisat2


Functional gene annotation:
GSEA, GO, KEGG, Panther


Variant calling:
samtools, GATK, MuTect

Variant annotation:
SnpEff, dbSNP, 1000 Genome, COSMIC, phyloP, ExAC

Peak calling & characterisation:
MACS2 peak calling (SICER for histones)
MEME/DREME motif search

Microarray:
Genotyping arrays
Expression arrays
Methylation arrays


Proteomics:
MaxQuant (novice)

Organisms:
Homo sapiens, Mus musculus, S. aureus, S. cerevisiae,
C. elegans, X. Iaevis, E. coli, D. melanogaster