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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.
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://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/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://ranger.sourceforge.net/
Software for a multi-purpose ChIP Seq peak caller.
Proper citation: PeakRanger (RRID:SCR_010863) Copy
http://biodoop-seal.sourceforge.net/
A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments.
Proper citation: SEAL (RRID:SCR_010914) Copy
http://cran.r-project.org/web/packages/DIME/index.html
R-package for identifying differential ChIP-seq based on an ensemble of mixture models.
Proper citation: DIME (RRID:SCR_010874) Copy
http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=CloudBurst
A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.
Proper citation: CloudBurst (RRID:SCR_010911) Copy
https://www.sanger.ac.uk/science/tools/caf
Software tools for manipulating Common Assembly Format files text format for describing sequence assemblies,that can be downloaded from the Sanger ftp site.
Proper citation: caftools (RRID:SCR_023982) Copy
http://ingenium.home.xs4all.nl/dicom.html
Software for DICOM training and testing,Demonstration and research image archives,Image format conversion from scanner with DICOM network access,DICOM image viewing and slide making, DICOM image selection, (limited) editing, and splitting and merging of series, Advanced scriptable image modification, filtering, forwarding and conversion, DICOM caching and archive merging, DICOM web access for viewing and data management (scriptable),Connection to Lua IDE for all sorts of DICOM manipulation.
Proper citation: Conquest DICOM (RRID:SCR_023993) Copy
https://github.com/pennsignals/chime
Software designed to assist hospitals and public health officials with understanding hospital capacity needs as they relate to the COVID pandemic. CHIME enables capacity planning by providing estimates of total daily and running totals of inpatient hospitalizations, ICU admissions, and patients requiring ventilation.
Proper citation: CHIME (RRID:SCR_023987) Copy
https://genome.sph.umich.edu/wiki/EMMAX
Software statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model.
Proper citation: EMMAX (RRID:SCR_024012) Copy
Software extensible open source radiation therapy research platform based on the DICOM standard. It also functions as a cross-platform DICOM RT viewer.
Proper citation: dicompyler (RRID:SCR_024006) Copy
https://cran.r-project.org/web/packages/foreign/index.html
Software tool for reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.
Proper citation: foreign (RRID:SCR_024025) Copy
https://github.com/rrwick/Deepbinner
Software tool for demultiplexing barcoded Oxford Nanopore sequencing reads.Signal level demultiplexer for Oxford Nanopore reads.
Proper citation: Deepbinner (RRID:SCR_024001) Copy
http://www.ncbi.nlm.nih.gov/tools/gbench/
An integrated application for viewing and analyzing sequence data.
Proper citation: NCBI Genome Workbench (RRID:SCR_011794) Copy
http://www.cs.utah.edu/~miriah/mizbee/Overview.html
A multiscale synteny browser for exploring conservation relationships in comparative genomics data.
Proper citation: MizBee (RRID:SCR_011804) Copy
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