There are many R software and bioconductor packages for NGS data analysis, some of them are as follows
The Biostrings package from Bioconductor provides an advanced environment for efficient sequence management and analysis in R. It contains many speed and memory effective string containers, string matching algorithms, and other utilities, for fast manipulation of large sets of biological sequences. The objects and functions provided by Biostrings form the basis for many other sequence analysis packages. Documentation
IRanges provides the low-level infrastructure and containers for handling sets of integer ranges within Bioconductor's BioC-Seq domain. Its classes and methods provide support for many more high-level packages like GenomicRanges, ShortRead, Rsamtools, etc. Documentation
The GenomicRanges package serves as the foundation for representing genomic locations within the Bioconductor project. It is built upon the IRanges infrastructure and defines three major data containers - GRanges, GRangesList and GappedAlignments - which are supporting other important BioC-Seq packages including ShortRead, Rsamtools, rtracklayer, GenomicFeatures and BSgenome. Compared to the IRanges container, the GRanges/GRangesList classes are more flexible and extensible to store additional information about sequence ranges, such as chromosome identifiers (sequence space), strand information and annotation data. Documentation
The cosmo package allows to search a set of unaligned DNA sequences for a shared motif that may function as transcription factor binding site. The algorithm extends the popular motif discovery tool MEME (Bailey and Elkan, 1995) in that it allows the search to be supervised by specifying a set of constraints that the motif to be discovered must satisfy. Documentation
BCRANK is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list. The algorithm was developed for detecting transcription factor (TF) binding sites in a large number of enriched regions from high-throughput ChIP-chip or ChIP-seq experiments, but it can be applied to any ranked list of DNA sequences. Documentation
rGADEM: Documentation
MotIV: Documentation
The ShortRead package provides input, quality control, filtering, parsing, and manipulation functionality for short read sequences produced by high throughput sequencing technologies. While support is provided for many sequencing technologies, this package is primairly focused on Solexa/Illumina reads. Documentation
Rsamtools provides functions for parsing and inspecting samtools BAM formatted binary alignment data. SAM/BAM is quickly becoming a universal standard alignment format, and is now supported by a wide variety of alignment tools. Documentation
Samtools Website
BWA (Burrows-Wheeler Alignment) Website
Additional tools for SNP analysis:
BSgenome provides an object oriented infrastructure for interacting with a Biostring based genome sequence. BSgenome packages exist for many common genomes, and can be created to represent custom genomes. See the "How to forge a BSgenome data package" Vignette for instructions to create a new BSgenome package if a prebuilt package does not exist for your organism. Documentation
rtracklayer provides an interface for exporting annotation feature data to various genome browsers and file formats (such as GFF). See the Small RNA Profiling exercise for an example of using rtracklayer to visualize alignment coverage. Documentation
The biomaRt package, provides an interface to a growing collection of databases implementing the BioMart software suite (http:// www.biomart.org). The package enables online retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas. This data is retrieved automatically via the Internet, so it's recommended that you cache the data locally, or check versions if your code will be adversely affected by updates to these data. Documentation
Bioconductor provides various packages for analyzing and visualizing ChIP-Seq data. Only a small selection of these packages is introduced here. Additional useful introductions to this topic are: BioC ChIP-seq Case Study and BioC ChIP-Seq.
The chipseq package combines a variety of HT-Seq packages to a pipeline for ChIP-Seq data analysis. Documentation
BayesPeak is a peak calling package for identifying DNA binding sites of proteins in ChIP-Seq experiments. Its algorithm uses hidden Markov models (HMM) and Bayesian statistical methods. The following sample code introduces the identification of peaks with the BayesPeak package as well as the incorporation of read coverage information obtained by the chipseq package. Documentation [ Publication ]
The PICS package applies probabilistic inference to aligned-read ChIP-Seq data in order to identify regions bound by transcription factors. PICS identifies enriched regions by modeling local concentrations of directional reads, and uses DNA fragment length prior information to discriminate closely adjacent binding events via a Bayesian hierarchical t-mixture model. The following sample code uses the test data set from the above BayesPeak package in order to compare the results from both methods by identifying their consensus peak set. Documentation [ Publication ]
The ChIPpeakAnno package provides. batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. It includes functions to retrieve the sequences around peaks, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. The package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages. Documentation
DiffBind: Documentation
MOSAICS: Documentation
iSeq: Documentation
ChIPseqR: Documentation
ChiPsim: Documentation
CSAR: Documentation
ChIP-Seq Pipeline: PICS, rGADEM and MotIV (developer web site)
SPP: ChIP-seq processing pipeline
The GenomicRanges package provides support for importing into R short read alignment data in BAM format (via Rsamtools) and associating them with genomic feature ranges, such as exons or genes. This way one can quantify the number of reads aligning to annotated genomic regions. The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome. The two main functions for read counting provided by this infrastructure are countOverlaps and summarizeOverlaps. For their proper usage, it is important to read the corresponding PDF manual. Documentation
The DESeq package contains functions to call differentially expressed genes (DEGs) in count tables based on a model using the negative binomial distribution. It expects as input a data frame with the raw read counts per region/gene of interest (rows) for each test sample (columns). Such a count table can be imported into R or generated from BAM alignment files using the countOverlaps function as introduced above. Documentation
The edgeR package uses empirical Bayes estimation and exact tests based on the negative binomial distribution to call differentially expressed genes (DEGs) in count data.
A variety of additional R packages are available for normalizing RNA-Seq read count data and identifying differentially expressed genes (DEG):
easyRNASeq (simplifies read counting per genome feature)
DEXSeq (Inference of differential exon usage); parathyroidSE explains how to generate exon read counts in R
baySeq (also see: segmentSeq)
Genominator (Bullard et al. 2010)
ggbio: ggplot2 extension for genomics data (online manual) Gviz: Plotting data and annotation information along genomic coordinates HilbertVis: Hilbert genome plots
GenomeGraphs: Plotting genomic information from Ensembl
TileQC: Flow Cell Quality Visualization
rtracklayer: R interface to genome browsers
genoPlotR: Plotting maps of genes and genomes
Genominator: Tools for storing, accessing, analyzing and visualizing genomic data.
To install all packages
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite(c("ShortRead", "Biostrings", "IRanges", "BSgenome", "rtracklayer", "biomaRt", "chipseq", "ChIPpeakAnno", "Rsamtools", "BayesPeak", "PICS", "GenomicRanges", "DESeq", "edgeR", "leeBamViews", "GenomicFeatures", "BSgenome.Celegans.UCSC.ce2"))
Comments
R package SPP for chip-seq analysis. It can read quite a few aligner's output file. Here is the original package tutorial. http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html
Here is my version of the tutorial:
https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/
SRAdb: query and use public next-generation sequencing data from within R
http://www.biomedcentral.com/1471-2105/14/19
We generally receive some common question like ... where to find human reference genome? What is reference annotation, how to download it etc. Here are some resources that I found useful:
ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/
ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/Primary_Assembly/assembled_chromosomes/FASTA/
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/
Reference annotation download
http://useast.ensembl.org/info/data/ftp/index.html
UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples http://bioinformatics.oxfordjournals.org/content/early/2014/09/10/bioinformatics.btu607.abstract