class: center, middle, inverse, title-slide # Introduction to Bioconductor ## Pre-workshop Introduction to RNA-seq ### R-Ladies Tunis team ### 2020-09-10 --- class: center, middle # Introduction to Bioconductor --- background-image: url(https://alison.rbind.io/slides/images/rladies-r-logo.png) background-position: top right background-size: 110px 120px layout: true --- # Introduction - [Bioconductor](https://www.bioconductor.org/) https://www.bioconductor.org/ is an open source project for the analysis of biological and biomedical data. -- - It contains more than 1000 packages for example data, analysis tools, and development tools for building new packages. The bioconductor website https://www.bioconductor.org/ contains much more information on the project. <img src="Bioconductor.png" width="1263" /> --- # The Bioconductor Project <img src="Bioconductor1.png" width="75" /> The Bioconductor project is an open-source repository for R packages, datasets, and workflows that are specific for analyzing biological data. The broad goals of the Bioconductor project are: 1. To provide widespread access to a broad range of powerful statistical and graphical methods for the analysis of genomic data. -- 1. To facilitate the inclusion of biological metadata in the analysis of genomic data, e.g. literature data from PubMed, annotation data from Entrez genes. -- 1. To provide a common software platform that enables the rapid development and deployment of extensible, scalable, and interoperable software. -- 1. To train researchers on computational and statistical methods for the analysis of genomic data. --- # How to install Bioconductor The Bioconductor package collection forms its own repository and therefore is installed differently. <br> To install `core Bioconductor packages` you need to go to your Rstudio and type these lines of code in the console. ```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.11") ``` ``` ## Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 (2020-06-22) ``` ``` ## Installation path not writeable, unable to update packages: callr, jsonlite, ## stringi, xfun, MASS ``` --- # How to install Bioconductor(1) When you'll type these lines of code, you'll get this in the console.  --- # How to install Bioconductor(2)  --- # How to install a Bioconductor package To install a specific package, e.g., “DESeq2” we use the install() function from the BiocManager package. ```r BiocManager::install("DESeq2") ``` To install many packages: ```r BiocManager::install(c("airway","tximeta")) ``` --- class: inverse,center, middle # Social media LinkedIn : https://tinyurl.com/y8hlt5np Meetup : https://www.meetup.com/rladies-tunis/ Twitter : https://twitter.com/RLadiesTunis Instagram : https://www.instagram.com/rladiestunis/ Youtube_Channel : https://tinyurl.com/ycm48c6w Github : https://github.com/rladiestunis Facebook : https://www.facebook.com/RLadiesTunis/ --- class: inverse,center, middle # Thanks!