Overview
Objective of this course is to introduce you to Bioconductor for analysis of NGS based genomics data. Bioconductor repository contains several R packages that allow to perform rigorous statistical analyses and visualization of large-scale omics data.
Different types of analyses can be carried out using Bioconductor such as Genome/Exome sequencing, RNASeq, ChIPSeq, MethylSeq, Microarray based studies (Expression, SNP arrays), Functional annotations, Proteomics, Flow cytometry studies etc.
In this course we will teach you Bioconductor by taking whole genome/exome sequencing (WGS/WES) data analysis as case study. We will start with basic introduction to R, Rstudio and Bioconductor. This will be followed by exploring core Bioconductor packages such as BioStrings, GenomicRanges etc, upon which majority of other analysis packages depend. Next we will explore few annotation resources such as BSgenome, Org, TxDb packages. Last we will explore exome sequencing workflow (variant calling, annotation and visualization) through packages like ShortRead, RSamtools, VariantAnnotation etc.
Objective of this course is to introduce you to Bioconductor for analysis of NGS based genomics data. Bioconductor repository contains several R packages that allow to perform rigorous statistical analyses and visualization of large-scale omics data.
Different types of analyses can be carried out using Bioconductor such as Genome/Exome sequencing, RNASeq, ChIPSeq, MethylSeq, Microarray based studies (Expression, SNP arrays), Functional annotations, Proteomics, Flow cytometry studies etc.
In this course we will teach you Bioconductor by taking whole genome/exome sequencing (WGS/WES) data analysis as case study. We will start with basic introduction to R, Rstudio and Bioconductor. This will be followed by exploring core Bioconductor packages such as BioStrings, GenomicRanges etc, upon which majority of other analysis packages depend. Next we will explore few annotation resources such as BSgenome, Org, TxDb packages. Last we will explore exome sequencing workflow (variant calling, annotation and visualization) through packages like ShortRead, RSamtools, VariantAnnotation etc.
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