Supplementary Table 1. Survey of open-source ChIP-Seq analysis programs. References that also appear in the
main text are numbered accordingly. Supplementary references are indicated by S1 (etc) and NA indicates that the
program has not yet been published. Websites hosting the code are provided for each method, unless the code was
not publicly released at time of writing (usually available on request from authors).
Program
Ref.
Website
MACS
QuEST
Useq
Minimal
ChIPSeq
PeakFinder
XSET
"The ChipSeq
Peak Finder"
FindPeaks
TIROE
PeakSeq
GLITR
Sole-Search
E-RANGE
CisGenome
BayesPeak
spp (R package)
SISSRS
13
14
15
16
http://liulab.dfci.harvard.edu/MACS/
http://mendel.stanford.edu/SidowLab/downloads/quest/
http://useq.sourceforge.net/
http://woldlab.caltech.edu/html/software
Python
Perl
Perl, C
Python
17
18
Not publicly released
http://cmb.gis.a-star.edu.sg/ChIPSeq/paperChIPSeq.htm
C
19
20
21
22
23
27
28
30
31
32
http://vancouvershortr.sourceforge.net/
Not publicly released
http://www.gersteinlab.org/proj/PeakSeq/
http://web.me.com/kaestnerlab1/GLITR/
http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi
http://woldlab.caltech.edu/rnaseq/
http://www.biostat.jhsph.edu/~hji/cisgenome/
http://compbio.med.harvard.edu/Supplements/ChIP-seq/
http://sissrs.rajajothi.com/
Perl / C
Perl, Python
Perl, java
Python
C/C++
Perl / C
R
Perl
F-Seq
33
http://www.genome.duke.edu/labs/furey/software/fseq
java
SIPeS
24
C
CSDeconv
34
http://gmdd.shgmo.org/Computational-Biology/ChIPSeq/download/SIPeS
http://www.unisa.edu.au/maths/phenomics/csdeconv/
SWEMBL
GeneTrack
HPeak
ChIP-Peak
analysis server
Bioconductor
ChIPseq
25
S1
NA
NA
http://www.ebi.ac.uk/~swilder/SWEMBL/
http://code.google.com/p/genetrack/
http://www.sph.umich.edu/csg/qin/HPeak/
http://ccg.vital-it.ch/chipseq/
NA
http://www.bioconductor.org/workshops/2008/SeattleNov08/
http://www.compbio.group.cam.ac.uk/Resources/BayesPeak/csbayespeak.html
Language
java
MATLAB
R2009a
C
Perl
Web interface
R
Epigenetic Modifications Programs
ChipDiff
Chromasig
SICER
Models 1-3
CCAT
33
34
35
40
41
http://cmb.gis.a-star.edu.sg/ChIPSeq/paperChIPDiff.htm
http://bioinformatics-renlab.ucsd.edu/rentrac/wiki/ChromaSig
http://home.gwu.edu/~wpeng/Software.htm
http://gbic.biol.rug.nl/supplementary/2009/ChromatinProfiles/
http://cmb.gis.a-star.edu.sg/ChIPSeq/tools.htm
RNA Polymerase Programs
Finite Mixture
Model
Poisson Mixture
Model
31
Not publicly released
32
Not publicly released
C
Perl,C/C++
Python
R
C
Supplementary Reference:
S1.
Albert, I., et al. GeneTrack-a genomic data processing and visualization framework.
Bioinformatics 24, 1305-6 (2008).