Introduction to R/Bioconductor

Introduction to R/Bioconductor

The R/Bioconductor framework is the most widely used analysis tool for sequence based bioinformatics.

The lecture gives an overview of typical Bioconductor based analysis pipelines including:

  • Microarray and NGS data processing
  • Differential gene expression analysis
  • Working with sequence and annotation packages
  • Programmatic access to public databases
  • Visualization of genomic data

Each lecture is organized around one analysis question using publicly available data. It consist of 1 hour lecture and 1 hour hands on practical.

Participants should bring along their laptops.

Basic R knowledge is of an advantage.

For studensts: If you need credit points  please register at the Unibas Course Directory (Vorlesungsverzeichnis)!

Date Room Title Teacher
 
September 21, 2016 Pharmazentrum, Sitzungszimmer 1067 Revisions of R basics, bladder_cancer.tab Florian
 
September 28, 2016 Pharmazentrum, Sitzungszimmer 1067 Differential gene expression analysis with GEO2R Florian
 
October 05, 2016 Pharmazentrum, Sitzungszimmer 1067 Differential gene expression analysis I (microarray data) Robert
 
October 12, 2016 Pharmazentrum, Sitzungszimmer 1067 Differential gene expression analysis II (limma framework), GSE27114_GPL1261_eSet_RMA.rdsGSE27114_GPL6246_eSet_RMA.rds Robert
 
October 19, 2016 Pharmazentrum, Sitzungszimmer 1067 Annotation packages Robert
 
October 26, 2016 Pharmazentrum, Sitzungszimmer 1067 RNAseq I, from raw data to count data (01_SampleFile.txt, 03_QC_RNAseq.pdf, 03_SampleFile_bam.txt, 03_counts.txt, 03_counts_st.txt, ARTICLE_Tippmann-Schubeler_MolecularSystemsBiology_2012.pdf) Helene
 
November 02, 2016 Pharmazentrum, Sitzungszimmer 1067 RNAseq II, starting from count data, 07_counts.txt Atul
 
November 09, 2016 Pharmazentrum, Sitzungszimmer 1067 RNAseq III, Examples, comparison of array vs. RNAseq Atul
 
November 16, 2016 Biozentrum, Seminarraum 104 rtracklayer and different file formats, ChIP_promoter_counts.rds Sarah
 
November 23, 2016 Pharmazentrum, Sitzungszimmer 1067 ChIP-seq I, 10_ChIPseq_coverage_interactive.Rmd, 10_ChIPseq_coverage_shinyApp.R, ChIP_promoter_counts.rds Michael
 
November 30, 2016 Pharmazentrum, Sitzungszimmer 1067 ChIP-seq II, ChIP_promoter_counts.rds Michael
 
December 07, 2016 ZLF, Kleiner Hörsaal Bioconductor developer Meeting
 
December 14, 2016 Pharmazentrum, Sitzungszimmer 1067 Comparison of ChIPseq and RNAseq, full_chipseq_norm_counts.RDS, ES_peaks.bed, TN_peaks.bed Sarah
 
December 21, 2016 Pharmazentrum, Sitzungszimmer 1067 Q/A, romer_c2_results_TNvsES.rds, mouse_H_v5p2.rdata, mouse_c2_v5p2.rdata, aac7041_SM_Table_S4.csv, aac7041_SM_Table_S3.csv, aac7041_SM_Table_S2.csv, aac7041_SM_Table_S1.csv all

 

 

Next course (Autumn 2016)

Autumn Semester 2016

Wednesday 14:15 - 16:00

Starting on September 21st