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http://bioconductor.org/packages/2.1/bioc/html/arrayMagic.html

Software providing a collection of utilities for quality control and processing of two-colour cDNA microarray data

Proper citation: arrayMagic (RRID:SCR_010933) Copy   

•   Source: SciCrunch Registry
  

http://smithlab.usc.edu/plone/software/piranha

A peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Piranha (RRID:SCR_010903) Copy   

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http://methmarker.mpi-inf.mpg.de/

Tool that facilitates the design and optimization of gene-specific DNA methylation assays. Beyond its use as an epigenetic primer-design tool, it provides extensive support for epigenetic biomarker optimization. Download MethMarker or start it directly from within your web browser.

Proper citation: MethMarker (RRID:SCR_010908) Copy   

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http://www.stat.wisc.edu/~keles/Software/mosaics/

Software developed as a flexible mixture modeling approach for detecting peaks of one-sample (ChIP sample) or two-sample (ChIP sample and matched control sample) ChIP-seq data.

Proper citation: MOSAiCS (RRID:SCR_010861) Copy   

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http://sissrs.rajajothi.com/

Anl algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments.

Proper citation: SISSRs (RRID:SCR_010866) Copy   

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http://casp.rnet.missouri.edu/soydb/

A Knowledge Database of Soybean Transcription Factors. PSI-BLAST is available to find hits from the database.

Proper citation: SoyDB (RRID:SCR_010900) Copy   

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http://code.google.com/p/zinba/

Software to identify genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts.

Proper citation: ZINBA (RRID:SCR_010868) Copy   

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http://archive.igbmc.fr/recherche/Prog_FGC/Eq_HGron/Polyphemus.html

R package for comparative analysis of RNA Polymerase II ChIP-Seq profiles by non-linear normalization.

Proper citation: POLYPHEMUS (RRID:SCR_010870) Copy   

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http://ppseq.sourceforge.net/

A software suite including a scalable hierarchical multitasking parallel infrastructure and the classical sequencing algorithms.

Proper citation: PPSEQ (RRID:SCR_010913) Copy   

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http://adacgh.bioinfo.cnio.es/

A web tool for the analysis of aCGH data sets. They focus on calling gains and losses and estimating the number of copy changes. Note: ADaCGH will continue being maintained, but is deprecated. Their new tool for CGH and CNV is WaviCGH, http://wavi.bioinfo.cnio.es/

Proper citation: ADaCGH (RRID:SCR_010916) Copy   

•   Source: SciCrunch Registry
  

http://www.genomics.agilent.com/en/product.jsp?cid=AG-PT-111&tabId=AG-PR-1017&_requestid=587725

Software for a complete CGH and CGH+SNP microarray data analysis and data reporting solution to streamline the day-to-day cytogenetic sample analysis research workflow.

Proper citation: Agilent CytoGenomics software (RRID:SCR_010917) Copy   

•   Source: SciCrunch Registry
  

http://aroma-project.org/

An R package for analyzing large Affymetrix data sets.

Proper citation: Aroma.affymetrix (RRID:SCR_010919) Copy   

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http://code.google.com/p/diffreps/

Finding differential chromatin modification sites from ChIP-seq data.

Proper citation: diffReps (RRID:SCR_010873) Copy   

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http://www.webcitation.org/getfile?fileid=c6d148fcb4fde0ea6991ec319a7a3925d38f32bf

A software program which finds sequence elements conserved in a set of DNA sequences.

Proper citation: AlignACE (RRID:SCR_010875) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/p/arpeggio/wiki/Home/

Software for harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures.

Proper citation: Arpeggio (RRID:SCR_010876) Copy   

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http://autosome.ru/dichipmunk/

Software for motif discovery using dinucleotide position weight matrices (PWMs).

Proper citation: diChIPMunk (RRID:SCR_010879) Copy   

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http://kmersvm.beerlab.org/

A webserver built on the Galaxy framework that enables the mining of sequence data for transcription factor binding sites. This tool suite was designed to aid in analysis of next-generation sequencing (NGS) data that uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. While you may use datasets already available from Galaxy, you can upload your data using the ''Get Data'' Tool. The tool can upload data from a variety of locations.

Proper citation: kmer-SVM (RRID:SCR_010882) Copy   

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http://bioinfo.au.tsinghua.edu.cn/software/NURD/

An algorithm to inference isoform expression., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NURD (RRID:SCR_010988) Copy   

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http://www.ema.europa.eu/

An agency responsible for the evaluation and supervision of medicines developed by pharmaceutical companies for use in the European Union. Its main responsibility is the protection and promotion of public and animal health through the evaluation and supervision of medicines for human and veterinary use. The Agency also plays a role in stimulating innovation and research in the pharmaceutical sector. The Agency gives scientific advice and other assistance to companies for the development of new medicines. It publishes guidelines on quality-, safety- and efficacy-testing requirements. A dedicated SME Office provides special assistance to small and medium-sized enterprises.

Proper citation: European Medicines Agency (RRID:SCR_011215) Copy   

•   Source: SciCrunch Registry
  

http://hihg.med.miami.edu/software-download/seqem-version-1.0

Online tool for utilizing a genotype calling algorithm for next-generation sequence data.

Proper citation: SeqEM (RRID:SCR_002021) Copy   

•   Source: SciCrunch Registry