BRC Software Library

The following software is available (bold text items) or scheduled to be installed (in the order of listed priorities) in AGAR's software library. This software is accessible by setting up an AGAR user account. For a limited time these accounts are free; there will be a charge in the future. Access is through the computing lab in room 1226 at the Biotechnology Center.

Please let us know if there is another package you need!

High Priority

Bioconductor (for R) http://www.bioconductor.org/
(module) chippeakanno http://www.bioconductor.org/packages/2.5/bioc/html/ChIPpeakAnno.html
(module) degseq http://www.bioconductor.org/packages/2.6/bioc/html/DEGseq.html
(module) edger http://www.bioconductor.org/help/bioc-views/release/bioc/html/edgeR.html
(module) deseq http://www-huber.embl.de/users/anders/DESeq/
(module) shortread http://bioconductor.org/packages/release/bioc/html/ShortRead.html
(module) biostrings http://www.bioconductor.org/packages/2.2/bioc/html/Biostrings.html
Bedtools http://code.google.com/p/bedtools/
Blast+ http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
Bowtie http://bowtie-bio.sourceforge.net/
CLC Genomics Workbench
Clustal http://www.clustal.org/
Cufflinks http://cufflinks.cbcb.umd.edu/
FastX toolkit http://hannonlab.cshl.edu/fastx_toolkit/
Graphviz http://www.graphviz.org/
HOMER http://biowhat.ucsd.edu/homer/
IGV http://www.broadinstitute.org/software/igv/
MeV http://www.tm4.org/mev/
Muscle http://www.drive5.com/muscle/
QuEST http://mendel.stanford.edu/sidowlab/downloads/quest/
R http://www.r-project.org/
RSEM http://deweylab.biostat.wisc.edu/rsem/
Samtools http://samtools.sourceforge.net/
SSPACE http://www.baseclear.com/sequencing/data-analysis/bioinformatics-tools/sspace/
Tophat http://tophat.cbcb.umd.edu/
Velvet http://www.ebi.ac.uk/~zerbino/velvet/

Medium Priority

Abyss http://www.bcgsc.ca/platform/bioinfo/software/abyss
Allpaths (need to resolve GCC issue) http://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational-
bwa http://bio-bwa.sourceforge.net/
Blat http://users.soe.ucsc.edu/~kent/src/
Emacs
EMBOSS http://emboss.sourceforge.net/
GEdit
Hawkeye http://sourceforge.net/apps/mediawiki/amos/index.php?title=Hawkeye
IGV tools http://www.broadinstitute.org/software/igv/igvtools
ImageJ http://rsbweb.nih.gov/ij/
Maqview http://maq.sourceforge.net/maqview.shtml
Mauve http://gel.ahabs.wisc.edu/mauve/
OpenOffice.org Calc module
Partek (need to work out license etc.)
SeqMonk http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/
SOAP de novo http://soap.genomics.org.cn/soapdenovo.html
Staden http://staden.sourceforge.net/
Tablet http://bioinf.scri.ac.uk/tablet/
Tandem Repeats Finder http://tandem.bu.edu/trf/trf.html
vmatch http://www.vmatch.de/

Low Priority

bamtools http://sourceforge.net/projects/bamtools/
inGAP http://code.google.com/p/ingap/
LookSeq http://www.sanger.ac.uk/resources/software/lookseq/
mothur http://www.mothur.org/
Mochiview http://johnsonlab.ucsf.edu/sj/mochiview-software/
SeqBuster http://estivill_lab.crg.es/seqbuster/