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http://cran.r-project.org/web/packages/NAPPA/
Software that enables the processing and normalization of the standard mRNA data output from the Nanostring nCounter software.
Proper citation: NAPPA (RRID:SCR_003419) Copy
https://code.google.com/p/fade/
A software package designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome. FadE uses color reads produced by the SOLiD sequencer or nucleotide reads produced by the Illumina or 454 sequencing platforms.
Proper citation: FadE (RRID:SCR_003448) Copy
http://www.compgen.org/tools/metagen
Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression.
Proper citation: metagen (RRID:SCR_003443) Copy
http://ims.cochrane.org/revman/about-revman-5
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A software package that does meta-analysis and provides results in tabular format and graphically., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: RevMan (RRID:SCR_003581) Copy
http://bioinformatics.bc.edu/marthlab/wiki/index.php/PyroBayes
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A base caller for pyrosequences from the 454 Life Sciences sequencing machines.
Proper citation: PyroBayes (RRID:SCR_003757) Copy
http://genome.sph.umich.edu/wiki/RAREMETAL
A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing.
Proper citation: RAREMETAL (RRID:SCR_003573) Copy
http://web.bioinformatics.cicbiogune.es/AM/AnnotationModules.php
A tool for finding significant combinations of multisource annotations in gene lists.
Proper citation: Annotation-Modules (RRID:SCR_008025) Copy
http://biq-analyzer-ht.bioinf.mpi-inf.mpg.de/
Software that currently allows to process an amount of bisulfite sequencing reads obtained in one or several bisulfite sequencing experiments.
Proper citation: BiQAnalyzer HT (RRID:SCR_008045) Copy
http://erlichlab.wi.mit.edu/lobSTR/
A software tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: lobSTR (RRID:SCR_008030) Copy
http://drive5.com/usearch/manual/uchime_algo.html
An algorithm for detecting chimeric sequences.
Proper citation: UCHIME (RRID:SCR_008057) Copy
http://cran.r-project.org/web/packages/RJaCGH/index.html
Software for Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models.
Proper citation: RJaCGH (RRID:SCR_008381) Copy
http://www.cerc.utexas.edu/OnlineCall/
A fast basecalling scheme for Illumina''s Next Generation sequencing machines, specifically designed for GAII.
Proper citation: OnlineCall (RRID:SCR_008263) Copy
http://bioinfo.cipf.es/isacghtrac
Software to analyze CNV that will now normalize arrays CGH and it will visually integrate different genome annotations.
Proper citation: IsaCGH (RRID:SCR_008375) Copy
http://seqpig.sourceforge.net/
A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters.
Proper citation: SeqPig (RRID:SCR_008548) Copy
http://mothra.ornl.gov/cgi-bin/cat/cat.cgi
A repository of tools for analysis and annotation of CAZYmes (Carbohydrate Active enZYmes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CAT (RRID:SCR_008421) Copy
http://www.broadinstitute.org/scientific-community/science/programs/cancer/ultrasome
An efficient methodology for detecting and delineating gains and losses of chromosomal material in DNA copy-number data.
Proper citation: Ultrasome (RRID:SCR_008465) Copy
http://pga.mgh.harvard.edu/oligopicker/
Software to help selecting up to five oligo probes for each of the DNA sequences you provided for microarray spotting.
Proper citation: OligoPicker (RRID:SCR_008720) Copy
http://dc.crs4.it/projects/biodoop
A suite of parallel bioinformatics applications based upon a popular open-source Java implementation of MapReduce, Hadoop.
Proper citation: Biodoop (RRID:SCR_008711) Copy
http://code.google.com/p/drgap/
Designed to identify Driver Genes and Pathways in cancer genome sequencing studies.
Proper citation: DrGaP (RRID:SCR_008670) Copy
http://www.broadinstitute.org/cancer/cga/invex/
A permutation-based method (written in Python) for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations.
Proper citation: InVEx (RRID:SCR_008734) Copy
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