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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
A Perl based tool for the identification of differentially enriched regions in tiling microarray data.
Proper citation: BioTile (RRID:SCR_010953) Copy
A software package designed to automate the pipeline for analyzing site-level and region-level methylation changes in epigenetic studies utilizing the 450K DNA methylation microarray.
Proper citation: IMA (RRID:SCR_010955) Copy
http://www.cs.ubc.ca/~sshah/acgh/
A software for detection of DNA copy number alterations (CNAs) from array comparative genomic hybridization (aCGH) data.
Proper citation: CNA-HMMer (RRID:SCR_010924) Copy
http://bioinformatics.bioengr.uic.edu/TFBSGroup/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A Software program for Predicting Transcription Factor Binding Sites.
Proper citation: TFBSGroup (RRID:SCR_010887) Copy
http://www.softgenetics.com/CGHExplorer.html
An easy-to-use software tool for analyzing two color copy number alteration arrays from multiple platforms, including Agilent Technologies, Illumina, AffyMetrix, NimbleGen and others.
Proper citation: CGH Explorer (RRID:SCR_010920) Copy
http://owww.molgen.mpg.de/~abt_rop/molecular_cytogenetics/GenomeCAT.html
A software for the analysis and visualization of array CGH data.
Proper citation: CGHPRO (RRID:SCR_010921) Copy
http://cran.r-project.org/web/packages/cghseg/index.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Software R package dedicated to the analysis of CGH profiles using segmentation models.
Proper citation: CGHseg (RRID:SCR_010922) Copy
http://liulab.dfci.harvard.edu/NPS/
A python software package that can identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.
Proper citation: NPS (RRID:SCR_010890) Copy
A comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software.
Proper citation: BASE (RRID:SCR_010937) Copy
http://linus.nci.nih.gov/BRB-ArrayTools.html
An integrated software package for the visualization and statistical analysis of DNA microarray gene expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: BRB-ArrayTools (RRID:SCR_010938) Copy
A R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats.
Proper citation: nucleR (RRID:SCR_010895) Copy
http://genovar.sourceforge.net/
A Detection and Visualization software tool for Genomic Variants.
Proper citation: Genovar (RRID:SCR_010930) Copy
http://bcb.dfci.harvard.edu/~gcyuan/MAnorm/MAnorm.htm
A robust software package for quantitative comparison of ChIP-Seq data sets.
Proper citation: MAnorm (RRID:SCR_010869) Copy
http://zhanglab.c2b2.columbia.edu/index.php/MCarts
A hidden Markov model (HMM)-based software to predict clusters RNA motif sites.
Proper citation: mCarts (RRID:SCR_010902) Copy
http://software.big.ac.cn/MeRIP-PF.html
A high-efficiency and easy-to-use analysis pipeline for MeRIP-Seq peak-finding at high resolution, which compares distributions of reads between immunoprecipitation sample and control sample.
Proper citation: MeRIP-PF (RRID:SCR_010904) Copy
https://code.google.com/p/bsolana/
An approach for the analysis of two-base encoding bisulfite sequencing data.
Proper citation: B-SOLANA (RRID:SCR_010905) Copy
https://code.google.com/p/batmeth/
Improved mapper for bisulfite sequencing reads on DNA methylation.
Proper citation: BatMeth (RRID:SCR_010906) Copy
You can easily align, visualize and quantify bisulfite sequence data for CpG methylation analysis.
Proper citation: QUMA (RRID:SCR_010907) Copy
http://ww2.odu.edu/~nxkim/nextpeak/
A software program to call peaks from ChIP-seq data for transcription factor binding sites.
Proper citation: NEXT-peak (RRID:SCR_010862) Copy
http://ranger.sourceforge.net/
Software for a multi-purpose ChIP Seq peak caller.
Proper citation: PeakRanger (RRID:SCR_010863) Copy
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