margosolo/bioinformatics-r

Bioinformatics with R cookbook

Bioinformatics-R

Bioinformatics with R cookbook

This is for bioinformatics with R, the table of content as follow:

1.1 Getting started and installing libraries

1.2 Reading and writing

1.3 Filtering and subsetting data

1.4 Basic statistical operations on data

1.5 Genetating probability distributions

1.6 Performing statistical tests on data

1.7 Visualizing data

1.8 Working with PubMed in R

1.9 Retrieving data from BioMart

2.1 Installing packages from Bioconductor

2.2 Handing annotation databases in R

2.3 Performing ID conversion

2.4 The KEGG annotation of genes

2.5 The GO annotation of genes

2.6 The GO enrichment of genes

2.7 The KEGG enrichment of genes

3.1 Retreving a sequence

3.2 Reading and writing the FASTA file

3.3 Getting the detail of a sequence composition

3.4 Pairwise sequence alignment

3.5 Multiple sequence lignment

3.6 Phylogenetic analysis and tree plotting

3.7 Handing BLAST results

3.8 Pattern finding in a sequence

5.1 Reading CEL files

5.2 Building the ExpressionSet object

5.3 Handling the AffyBatch object

5.4 Checking the quality of data

5.5 Generating artificial expression data

5.6 Data normalization

5.7 Overcoming batch effects in expression data

5.8 An exploratory analysis of data with PCA

5.9 Finding the differentially expressed genes

5.10 Working with the data of multiple classes

5.11 Handling time series data

5.12 Fold changes in microarray data

5.13 The functional enrichment of data

6.1 The SNP association analysis

6.2 Running association scans for SNPs

6.3 The whole genome SNP association analysis