Course Overview

Course Integrity

This course is compiled automatically on 2021-07-16

The course is tested and available on MacOS, Windows and Ubuntu Linux for R version 4.1.0 (2021-05-18)



Overview

This course introduces the Bioconductor set of R packages.

The course consists of multiple sections, the first section introduces Bioconductor and remaining sections discuss the handling of Genomics data and metadata in R using Bioconductor packages. Each section is presented as HTML presentations or single page document. Exercises and answer sheets are included after all subsections to practice techniques and provide future reference examples..

Course material and exercises are available to view as rendered HTML at https://rockefelleruniversity.github.io/Bioconductor_Introduction/. All material is available to download under GPL v2 license.



Setting up


System Requirements

Install R

R can be installed from the R-project website.

The R website can be found here http://www.r-project.org/.

The download links and associated installation instructions for multiple platforms can be found below provided by Revolution Analytics. https://cran.revolutionanalytics.com

We recommend installing R 4.1.0 as this is the version used to compile the course. Direct downloads for R 4.1.0 for the main platforms can be found below:


Install RStudio

RStudio can be installed from the RStudio website.

http://www.rstudio.com/

RStudio can be downloaded for all platforms at the link below

https://rstudio.com/products/rstudio/download/


Install required packages

From the course package

install.packages('BiocManager')
BiocManager::install('RockefellerUniversity/Bioconductor_Introduction',subdir='BioconductorIntroduction')


From CRAN and Bioconductor

install.packages('BiocManager')
BiocManager::install('methods')
BiocManager::install('rmarkdown')
BiocManager::install('igraph')
BiocManager::install('org.Hs.eg.db')
BiocManager::install('RMariaDB')
BiocManager::install('Rbowtie')
BiocManager::install('parallel')
BiocManager::install('QuasR')
BiocManager::install('BSgenome')
BiocManager::install('BSgenome.Mmusculus.UCSC.mm10')
BiocManager::install('BSgenome.Hsapiens.UCSC.hg19')
BiocManager::install('BSgenome.Hsapiens.UCSC.hg38')
BiocManager::install('Biostrings')
BiocManager::install('rtracklayer')
BiocManager::install('ggplot2')
BiocManager::install('GenomicRanges')
BiocManager::install('ShortRead')
BiocManager::install('Rsubread')
BiocManager::install('Rsamtools')
BiocManager::install('Rbowtie2')
BiocManager::install('stringi')
BiocManager::install('Rhisat2')
BiocManager::install('R.utils')
BiocManager::install('GenomicAlignments')
BiocManager::install('basecallQC')
BiocManager::install('TxDb.Mmusculus.UCSC.mm10.knownGene')
BiocManager::install('TxDb.Hsapiens.UCSC.hg19.knownGene')
BiocManager::install('Rfastp')
BiocManager::install('TxDb.Hsapiens.UCSC.hg38.knownGene')
BiocManager::install('knitr')
BiocManager::install('testthat')
BiocManager::install('yaml')


Download the material

Download the material




The Presentations


Introduction to Bioconductor

This section introduces the Bioconductor set of R packages. Session sections:

  • Bioconductor overview
  • Packages for Genomics data
  • Package installation

Sequences in Bioconductor

In this session we introduce genomic sequence handling and import/export. Session sections:

  • Introduction to BSgenome packages
  • Manipulating sequence data using Biostrings package
  • Export/Import of FASTA files

Genomic Intervals in Bioconductor

In this session we introduce genomic interval handling and import/export. Session sections:

  • Introduction to GenomicRanges packages
  • Manipulating genomic intervals
  • Export/Import of BED files

Genomic Scores in Bioconductor

In this session we introduce genomic scores handling and import/export Session sections:

  • Importing and exporting bedGraph and bigWig files
  • Manipulating genomic scores in R
  • Operations and summary statitics using genomic scores

Genomic Features in Bioconductor

In this session we introduce genomic features handling and import/export. Session sections:

  • Importing and exporting Gene models as GTF/GFF
  • Working with TxDb objects
  • Retrieving annotation from OrgDb packages

FastQs in Bioconductor

In this session we introduce FastQ handling and import/export. Session sections:

  • Importing and exporting FastQ files
  • Quality assessment of FastQ files
  • Trimming and duplicate removal

Alignment in Bioconductor

In this session we introduce alignment in Bioconductor. Session sections:

  • Genomic and Splice aware alignment
  • QuasR, Rbowtie2 and Rsubread packages
  • Sorting and indexing BAM files

Aligned data in Bioconductor

In this session we introduce aligned data in Bioconductor. Session sections:

  • Import and export of BAM files
  • Reads as GAlignment objects
  • Conversion between GAlignment and GRanges objects

Summarizing aligned data in Bioconductor

In this session we introduce summarization of aligned data in Bioconductor. Session sections:

  • Creating coverage from BAM
  • Counting reads in regions
  • Summarising counts from large BAM files

Getting help


Course help

For advice, help and comments for the material covered in this course please contact us at the issues page associated to this course.

The link to the help pages can be found here


General Bioinformatics support

If you would like contact us about general bioinformatics advice, support or collaboration, please contact us the Bioinformatics Resource Center at .