Archives AVIESAN-IFB

Programme EBA-V4 2015 du 27 septembre au 02 octobre 2015

 

Cours généraux

Sujet Intervenant(s) PDF
NGS: the basics  T. Grange Download
Introduction to next-generation sequencing C. Thermes Download
Le cloud IFB et son instance Galaxy C. Blanchet Download
Vos traitements bioinformatiques avec Galaxy S. Maman, M. Bernard Download
Galaxy initiation A. Lermine Download
Visualization of Next Generation Sequencing Data using the Integrative Genomics Viewer (IGV) A. Lermine Download
Algorithmes de mapping M. Zytnicki Download

 

Variants

Sujet Intervenant(s) PDF
DNA-seq analysis : From raw reads to processed alignments E. Girard Download
Variant Filtering N. Lapalu Download
TP - Filtrage de Variants N. Lapalu Download
Variant Calling GATK S. Marthey Download
Pipeline d'annotation des variants M. Bernard, R. Legendre, S. Rodriguez Download
TP - Pipeline d'annotation des variants M. Bernard, R. Legendre, S. Rodriguez Download
Genomic Copy-Number Analysis B. Job Download
Copy Number Variations Detection - TD B. Job Download

 

RNA-seq

Sujet Intervenant(s) PDF
Analyse différentielle de données RNA-Seq : planification, description, exploration et modélisation H. Varet Download
TP RNA-seq : Differential expression analysis C. Billerey Download
Isoform detection and quantification from RNA-Seq data T. Dayris, C. Toffano-Nioche Download

 

ChIP-seq

Sujet Intervenant(s) PDF
Tutorials: ChIP-seq data analysis D. Puthier Link
ChIP-seq analysis M. Defrance, C. Herrmann, S. Le Gras, D. Puthier, M. Thomas.Chollier Download
ChIP-seq Annotation and Visualization - How to add biological meaning to peaks M. Defrance, C. Herrmann, D. Puthier, M. Thomas-Chollier, S. Le Gras, J. van Helden Download
Regulatory Sequence Analysis Tools (RSAT) J. van Helden Link
ChIP-seq: Discovering motifs in peak sequences J. van Helden Download

 

Cours généraux

Sujet Intervenant(s) PDF
Statistiques NGS avec R, un premier contact intuitif NGS statistics with R: an intuitive primer J. van Helden Link
Assemblage de-novo de transcriptome - Trinity E. Corre Download
RNA‐seq de novo E. Corre Download
Eukaryotic small RNA - Small RNAseq data analysis for miRNA identification P. Bardou, C. Gaspin, J. Mariette, O. Rué, M. Zytnicki Download
Commandes Unix : pour les débutants D. Puthier, M. Defrance, S. Le Gras, C. Blanchet Download
Link

Programme EBA-V4 d'octobre 2014

Plaquette au format PDF ou DOCX

Programme au format PDF

 

Cours généraux

Sujet Intervenant(s) Slides
Introduction to NGS C. Thermes PDF
NGS : the basics T. Grange PDF
Mapping Algorithms M. Zytnicki PDF - Notes
Visualization with the Integrative Genomics Viewer (IGV) - TP É. Girard PDF
A short Introduction to UCSC Genome Browser N. Servant PDF
Advanced workflow management M. Zytnicki PDF
Initiation aux libraires Galaxy G. Le Corguille PDF
Statistical challenges in data analysis J. Aubert PDF

 

Galaxy

Sujet Intervenant(s) Slides
Infrastucture Galaxy C. Caron PDF
Vos traitements bioinformatiques avec GALAXY M. Bernard PDF
GALAXY INITIATION - TP A. Lermine PDF
Pipeline d’annotation des variants génétiques S. Rodriguez et M. Bernard PDF
Pipeline d’annotation des variants génétiques sous Galaxy - TP S. Rodriguez et M. Bernard PDF
Advanced workflow management M. Zytnicki PDF
Initiation aux libraires Galaxy G. Le Corguille PDF

 

Variants

Sujet Intervenant Slides
DNA-seq analysis, From raw reads to processed alignments É. Girard PDF
Variant Filtering N. Lapalu PDF
Atelier Détection de Variants - TP Filtrage de Variants N. Lapalu PDF
Détection de varians (Variant calling) O. Sand PDF
Variant Calling avec GATK - TP O. Sand PDF
Statistics (and Algorithms) for Change-Point Detection in Genomics: Detection of CNV and others S. Robin PDF

 

RNA-Seq

Sujet Intervenant Slides
RNA-seq with reference genome : What kind of information can be extracted from it ? M. Deloger PDF
Differential expression analysis - TP M. Deloger PDF
RNA-seq with reference genome : What about transcripts reconstruction ? M. Deloger PDF
Splicing variants analysis M. Deloger PDF
Assemblage de-novo de transcriptome E. Corre PDF
Assemblage de-novo de transcriptome - TP E. Corre PDF

 

ChIP-Seq

Sujet Intervenant(s) Slides
ChIP-seq Analysis C. Herrmann PDF
ChIP-seq Annotation and Visualization: How to add biological meaning to peaks M. Defrance, M. Thomas-Chollier, C. Herrmann et D. Puthier PDF
Détection de motifs dans les pics ChIP-seq M. Thomas-Chollier, M. Defrance, C Herrmann et D. Puthier PDF

 

Cloud IFB

Sujet Intervenant Slides
Institut Français de Bioinformatique, Un cloud au service du vivant C. Blanchet PDF
Utilisation du cloud IFB C. Blanchet PDF

 

Exposés d'ouverture

Sujet Intervenant(s) Slides
Séquencage RAD tags, mise en oeuvre et applications E. Pante PDF
Introduction to non coding RNA C. Gaspin PDF

Programme EBA-V2 de Novembre 2013

Programme au format PDF ou DOCX

Plaquette au format PDF ou DOCX

General Talks

Sujet Intervenant Slides
The station biologique de Roscoff: a brieve introduction B. Kloareg PDF
Bioinformatique sur cloud: cas d'usage avec le portail Galaxy C. Blanchet PDF
Old generation statistics for next generation sequencing J. Van Helden PDF
Mapping Algorithms M. Zytinicki PDF
Introduction to NGS C. Thermes PDF
NGS: the basics T. Grange PDF
Statistical challenges in RNA-Seq data analysis J. Aubert PDF
Introductions aux formats de fichiers A. Lermine, O. Inizan PDF

 

Galaxy

Sujet Intervenant(s) Slides
Introduction à Galaxy A. Lermine, O. Inizan PDF
Initiation to Galaxy: Variant detection into chromosome 4 of the human genome A. Lermine PDF
 

Variants

Sujet Intervenant Slides
Pipeline d'annotation des variants génétiques S. Rodriguez, M. Bernard PDF
Mapping Exome-seq data E. Girard PDF
Le contrôle de la qualité sur les données fastq O. Inizan PDF
Variant calling in Exome-seq data using Varscan E. Girard PDF
Atelier détection des variants: filtrage des variants S. Gallina PDF
Atelier détection des variants: filtrage des variants - TP S. Gallina PDF
Development of a workflow for SNP detection: MAPHIT N. Choisne PDF
MAPHIT Tutorial - TP N. Choisne PDF
Genome Analysis Toolkit S. Marthey, O. Rué PDF
Variant calling in RNA-seq data using Varscan E. Girard PDF
Pipeline d'annotation des variants génétiques S. Rodriguez, M. Bernard PDF
Pipeline d'annotation des variants génétiques sous Galaxy - TP S. Rodriguez, M. Bernard PDF
Preprocessing et Variant Calling avec GATK - TP S. Marthey PDF
Complete Genome Analysis: structural variation detection A. Lermine PDF
Statistics for Change-Point Detection in Genomics: Detection of CNV and others R. Lebarbier PDF
Identify structural variants with SVDetect ?? PDF
Complete Genome Analysis: Detection of copy number alterations and loss of heterozygosity A. Lermine PDF
Identifying copy number alterations and genotype with Control-FREEC A. Lermine PDF

 

RNA-Seq

Sujet Intervenant Slides
Analysis of RNA-seq Data C. Chen PDF
Protocol for RNA-seq session C. Chen PDF
A New pipeline for differential expression Y. Luo PDF
Analysis of RNA-seq data D. Naquin, C. Chen PDF
What can you do with S-MART to analyze your RNA-Seq data M. Zytnicki PDF
RNA-Seq Analysis: de novo assembly E. Corre PDF
RNA-Seq Analysis: de novo assembly - TP E. Corre PDF
Assemblage de novo de transcriptomes E. Corre PDF
RNA-Seq de novo - TP E. Corre PDF
small RNA-seq data analysis: miRNA detection P. Bardou, W. Carré, C. Gaspin, S. Maman, J. Mariette, O. Rué PDF
Formation sRNA-Seq: Analysis des miRNAs sous Galaxy P. Bardou, I. Nabihoudine, C. Gaspin, O. Rué, S. Maman PDF
Hands-on session: smallRNA-seq N. Servant PDF

 

ChIP-seq

Sujet Intervenant Slides
Motif based analysis of ChIP-seq peaks or Did we loose the genetic switch? J. Van Helden PDF
Practical: motif analysis on ChIP-seq peaks J. Van Helden PDF
Protocol: annotation of ChIP-seq peaks ?? PDF
Protocol: peak-calling for ChIP-seq data / segmentation analysis for histone modification data J. Van Helden PDF
Integrated analysis of sequencing data: how to combine *-seq data M. Defrance PDF
Nebula - A web-server for advanced ChIP-seq data analysis V. Boeva PDF
ChIP-seq Analysis J. Van Helden, M. Defrance, C. Herrmann, D. Puthier, N. Servant, M. Thomas-Chollier, O.Sand PDF
Functional annotation of ChIP-peaks ?? PDF
Interpretation of ChIP-seq and ChIP-exo data M. Thomas-Chollier PDF
Evaluation de la qualité des pics sur base de la densité de reads M. Thomas-Chollier PDF
ChIP-seq Analysis ?? PDF

 

Programme EBA-V1 de janvier 2013

Plaquette au format PDF

Programme au PDF ou Docx

 

General talks

Sujet Intervenant Téléchargement(s)
Accueil Christine Lemaitre PDF ou PPT
NGS: the basics Thierry Grange PDF ou PPT
Algorithmes de mapping Matthias Zytnicki PDF
Introduction to NGS Claude Thermes PDF
Statistical challenges in RNA-seq data analysis Julie Aubert PDF

 

Galaxy

Sujet Intervenant(s) Téléchargement
Introduction à Galaxy Alban Lermine et Olivier Inizan PDF
TP Initiation à galaxy: "Variant detection of the chromosome 4 of the human genome" Alban Lermine PDF

 

CNV

Sujet Intervenant Téléchargement
TP Detection des CNV - Description  ?? PDF
TP Detection des CNV - Protocole  ?? PDF
TP Detection des CNV - Topo Bastien Job PDF
Statistic for Change-Point Dectection in Genomics Stéphane Robin PDF
Pipeline d'annotation des variants génétiques Sabrina Rodriguez et Maria Bernard PDF
SVDetect: a tool to identify genomics structural variations Bruno Zeitouni PDF
SVDetect TP Bruno Zeitouni PDF

 

RNA-Seq

Sujet Intervenant Téléchargement
RNASeq Analysis: de novo assembly Erwan Corre PDF
Protocol to identify the genes differentially expressed in 2 human cell lines Delphine Naquin PDF
What can you do with S-MART to analyze your RNA-seq data Mathias Zytnicki PDF

 

ChIP-Seq

Sujet Intervenant Téléchargement
Chip-Seq Analysis J. Van Helden PDF

 

Liste des intervenants

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