| ANNOVAR |
www.openbioinformatics.org/annovar/ |
| BEDOPS |
https://bedops.readthedocs.org/ |
| Bedtools |
http://bedtools.readthedocs.org/en/latest/ |
| Biomart |
http://www.ensembl.org/biomart/ |
| Biowulf |
https://hpc.nih.gov |
| Bowtie2 |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| CADD database |
http://cadd.gs.washington.edu/ |
| ChIPQC |
https://github.com/Bioconductor-mirror/ChIPQC |
| CuffDiff 2 |
http://cole-trapnell-lab.github.io/cufflinks/cuffdiff |
| Cufflinks |
http://cole-trapnell-lab.github.io/cufflinks |
| Cutadapt |
http://dx.doi.org/10.14806/ej.17.1.200 |
| dbSNP |
http://www.ncbi.nlm.nih.gov/SNP/ |
| DiffBind |
http://bioconductor.org/packages/release/bioc/html/DiffBind.html |
| Diffsplice |
http://www.netlab.uky.edu/p/bioinfo/DiffSplice |
| DREME |
http://meme-suite.org/tools/dreme |
| DSGseq |
http://bioinfo.au.tsinghua.edu.cn/software/DSGseq |
| EdgeR |
https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| ESP6500 |
http://evs.gs.washington.edu/EVS/ |
| ExAC |
http://exac.broadinstitute.org/ |
| FastQC |
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| FASTX-Toolkit |
http://hannonlab.cshl.edu/fastx_toolkit/index.html |
| F-Seq |
https://github.com/aboyle/F-seq |
| Hotspot |
https://github.com/rthurman/hotspot |
| HPeak |
http://csg.sph.umich.edu//qin/HPeak/ |
| MACS2 |
https://github.com/taoliu/MACS |
| MATS |
http://rnaseq-mats.sourceforge.net |
| MEME |
http://meme-suite.org/tools/meme |
| NGS QC Toolkit |
http://www.nipgr.res.in/ngsqctoolkit.html |
| Oases |
http://www.ebi.ac.uk/~zerbino/oases |
| ODIN |
http://www.regulatory-genomics.org/odin-2/basic-introduction/ |
| PeakSeq |
http://info.gersteinlab.org/PeakSeq |
| Peakzilla |
https://github.com/steinmann/peakzilla |
| Picard |
http://broadinstitute.github.io/picard/ |
| Profiling (GERP) score. |
http://mendel.stanford.edu/SidowLab/downloads/gerp/ |
| Retnet |
https://sph.uth.edu/retnet/home.htm |
| RNA-STAR |
http://code.google.com/p/rna-star/ |
| Samtools |
http://samtools.sourceforge.net/ |
| Scripture |
https://www.broadinstitute.org/software/scripture |
| SnpEff and |
http://snpeff.sourceforge.net/ |
| SplicingCompass |
http://www.ichip.de/software/SplicingCompass.html |
| SPP |
https://github.com/hms-dbmi/spp |
| STAR |
https://github.com/alexdobin/STAR |
| Tophat |
https://ccb.jhu.edu/software/tophat/index.shtml |
| Trimmomatic |
http://www.usadellab.org/cms/?page=trimmomatic |
| Trinity |
https://github.com/trinityrnaseq/trinityrnaseq/wiki |
| Variant Effect Predictor |
http://www.ensembl.org/Homo_sapiens/Tools/VEP |
