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