Bioinformatics tool URLs

R: https://www.r-project.org/

Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/

Bowtie: http://bowtie-bio.sourceforge.net/index.shtml

SRA ToolKit: https://github.com/ncbi/sra-tools

fastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Picard: http://broadinstitute.github.io/picard/

SAMTools: http://www.htslib.org/

deepTools: http://deeptools.readthedocs.org/en/latest/

BEDTools: http://bedtools.readthedocs.org/en/latest/

MACs tools: https://github.com/taoliu/MACS

HOMER tools: http://homer.salk.edu/homer/

Tophat: https://ccb.jhu.edu/software/tophat/manual.shtml

featureCounts: http://bioinf.wehi.edu.au/featureCounts/

IGVTools: https://www.broadinstitute.org/igv/igvtools

IGV browser: https://www.broadinstitute.org/igv/

UCSC browser: http://genome.ucsc.edu/

UCSC tools: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

DAVID: https://david.ncifcrf.gov/home.jsp

REVIGO tool: https://revigo.irb.hr/