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http://rnbeads.bioinf.mpi-inf.mpg.de/

An R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution, including Infinium 450K microarray and bisulfite sequencing protocols, but also MeDIP-seq and MBD-seq., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RnBeads (RRID:SCR_010958) Copy   

•   Source: SciCrunch Registry

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

A software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which is featured as multiple core parallel computing.

Proper citation: FastDMA (RRID:SCR_010954) Copy   

•   Source: SciCrunch Registry

http://www.illumina.com/software/illumina_connect.ilmn

Software that estimates copy number and annotates regions with copy number variants(CNV).

Proper citation: CNVPartition (RRID:SCR_010925) Copy   

•   Source: SciCrunch Registry

http://www.stats.ox.ac.uk/~giannoul/GenoSNP/

A genotyping algorithm for the Illumina Infinium SNP genotyping assay.

Proper citation: GenoSNP (RRID:SCR_010928) Copy   

•   Source: SciCrunch Registry

http://rsat.ulb.ac.be/

Software tool that predicts motifs in full-size peak sets. It performs all steps from motif discovery to visualization of the predicted sites in genome browsers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RSAT peak-motifs (RRID:SCR_010886) Copy   

•   Source: SciCrunch Registry

http://cisreg.cmmt.ubc.ca/TFFM/doc/

Software for Transcription Factor Flexible Models (TFFMs) that represent Transcription Factor Binding Sites (TFBSs) and are based on hidden Markov models (HMM). They are flexible and are able to model both position interdependence within TFBSs and variable length motifs within a single dedicated framework.

Proper citation: TFFM (RRID:SCR_010888) Copy   

•   Source: SciCrunch Registry

http://www.cs.ucr.edu/~polishka/

A command line software tool for accurate placing of the nucleosomes using a Modified Gaussian Mixture Model. It was designed to resolve overlapping nucleosomes and extract extra information (fuzziness, probability, etc.) of nucleosome placement. To achieve this goal the tool clusters the input tags according to Nucleosome Model (see the paper for detailed description) using EM learning process. The tool is written in C++. There are no special requirements except for g++ compiler and *nix environment to compile and use the tool. It was checked to compile using g++ compiler under Ubuntu 11.04 and Mac OS X 10.6

Proper citation: NOrMAL (RRID:SCR_010889) Copy   

•   Source: SciCrunch Registry

http://www.stat.wisc.edu/~keles/Software/demo_Nucde.pdf

An R package mapping nucleosome-linker boundaries from both MNase-Chip and MNase-Seq data using a non-homogeneous hidden-state model based on first order differences of experimental data along genomic coordinates.

Proper citation: NucDe (RRID:SCR_010893) Copy   

•   Source: SciCrunch Registry

https://launchpad.net/asterias

A set of web-based applications for the analysis of genomic and proteomic data. Asterias combines Python with R and C/C++, using MPI for parallelization, and aspires to become a standard for high-performance, distributed, web-based bioinformatics and biostatistics applications.

Proper citation: Asterias (RRID:SCR_010936) Copy   

•   Source: SciCrunch Registry

http://chipster.csc.fi/

A user-friendly analysis software for high-throughput data.

Proper citation: Chipster (RRID:SCR_010939) Copy   

•   Source: SciCrunch Registry

http://epigen.molgen.mpg.de/nuchunter/

Software for inferring nucleosome positions with their histone mark annotation from ChIP data. It is a versatile tool that can be used to predict positioned nucleosomes from one or multiple ChIP-seq bam files and it can be also used in conjunction with a control experiment.

Proper citation: NucHunter (RRID:SCR_010894) Copy   

•   Source: SciCrunch Registry

http://pfgrc.jcvi.org/index.php/bioinformatics/ginkgo.html

A spotted microarray data pre-processing platform featuring analysis functionalities for CGH and expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Ginkgo (RRID:SCR_010931) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry