High-Throughput Sequencing Analysis with Bioconductor

This was a semester course I taught to students from the PhD in Biomedical Sciences program at the Center for Genomic Sciences (UNAM). I had a lot of fun teaching this course as most of the students were already my friends and everyone was highly motivated to learn more. It sure was peculiar to teach a PhD level course when I had not enrolled in a PhD program myself yet! First of all, please check the syllabus PDF for the course before proceeding. Note that a basic knowledge of R was a prerequisite before joining the course. Below you will find links for most of the material.


Lectures

  1. R review PDF R and answers to the exercises PDF R. (English)
  2. Understanding the technology. PPT (English)
  3. Understanding the technology part II. PPT (English)
  4. Bioconductor. PDF R (English)
  5. Reproducibility. PDF R latsampX.txt files R (English)
  6. Infrastructure for Input/Output 01: ShortRead, Rsamtools. PDF R data files R (English)
  7. Infrastructure for Input/Output 02: IRanges, GenomicRanges. PDF R qual.Rdata R and na19240.Rda R (English)
  8. Infrastructure for Input/Output 03: Practice. PDF R data files (small version only) R (English)
  9. ChIP-seq overview. PDF R H3K4me3_chr16.bed.zip R Input_chr16.bed.zip R out.Rdata R (English)
  10. GenomeGraphs and rtracklayer. PDF R data.Rdata R EcoliGenes.Rdata R (English)

Spanish = material in Spanish. English = material in English.

Contact

  • Address: 615 N. Wolfe Street, Room E3032, Baltimore MD 21205-2179, United States
  • Office Phone: (410) 614 - 5424. It is best to contact me by email!
  • Email: lcollado ^^ jhsph DOT edu
  • Fax: (410) 955 - 0958.
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