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Facult茅 de m茅decine Facult茅 de m茅decine

Bioinformatics Support Platform for data analysis

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

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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
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Data managment (organize, archive, share)
Data submission (, )
High Performance Computing (cluster )
Mathematical Modelisation
Machine Learning (including deep-learning with torch)
Databases query
Data integration
Big Data File Handling ( format)
Data browsing web site ()
 

Reproducible Science Tools:



 

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