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https://github.com/macs3-project/MACS

Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.

Proper citation: MACS (RRID:SCR_013291) Copy   

•   Source: SciCrunch Registry

http://bioinfo.ctb.pku.edu.cn/MAP/

This resource is out of service. Documented on February 23,2021. Software for de novo metagenomic assembly program for shotgun DNA reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MAP (RRID:SCR_013216) Copy   

•   Source: SciCrunch Registry

http://genetics.bwh.harvard.edu/pph2/

Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs.

Proper citation: PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/crossbow/index.shtml

A scalable software pipeline for whole genome resequencing analysis.

Proper citation: Crossbow (RRID:SCR_013306) Copy   

•   Source: SciCrunch Registry

http://tomcatbackup.esat.kuleuven.be/inclusive/

A suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.

Proper citation: INCLUSive (RRID:SCR_013488) Copy   

•   Source: SciCrunch Registry

http://hannonlab.cshl.edu/Alta-Cyclic/main.html

An Illumina Genome-Analyzer (Solexa) base caller.

Proper citation: Alta-Cyclic (RRID:SCR_013373) Copy   

•   Source: SciCrunch Registry

http://www.osirix-viewer.com/

:OsiriX is an image processing software dedicated to DICOM images (.dcm / .DCM extension) produced by medical equipment (MRI, CT, PET, PET-CT, ...) and confocal microscopy (LSM and BioRAD-PIC format). It can also read many other file formats: TIFF (8,16, 32 bits), JPEG, PDF, AVI, MPEG and Quicktime. It is fully compliant with the DICOM standard for image comunication and image file formats. OsiriX is able to receive images transferred by DICOM communication protocol from any PACS or medical imaging modality (STORE SCP - Service Class Provider, STORE SCU - Service Class User, and Query/Retrieve) . OsiriX has been specifically designed for navigation and visualization of multimodality and multidimensional images: 2D Viewer, 3D Viewer, 4D Viewer (3D series with temporal dimension, for example: Cardiac-CT) and 5D Viewer (3D series with temporal and functional dimensions, for example: Cardiac-PET-CT). The 3D Viewer offers all modern rendering modes: Multiplanar reconstruction (MPR), Surface Rendering, Volume Rendering and Maximum Intensity Projection (MIP). All these modes support 4D data and are able to produce image fusion between two different series (for example: PET-CT). Osirix is at the same time a DICOM PACS workstation for medical imaging and an image processing software for medical research (radiology and nuclear imaging), functional imaging, 3D imaging, confocal microscopy and molecular imaging. :

Proper citation: OsiriX Medical Imaging Software (RRID:SCR_013618) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ai.sri.com/ptools/

A software application which supplies software tools to develop and maintain pathway/genome databases (PGDBs). These include the development of organism-specific databases, metabolic reconstruction and metabolic-flux modeling, scientific visualization and web publishing of organism-specific databases, analysis of gene-expression and metabolomics datasets, comparative genome and pathway analyses, and analysis of biological networks.

Proper citation: Pathway Tools (RRID:SCR_013786) Copy   

•   Source: SciCrunch Registry

http://mirdb.org/miRDB/

An online database for miRNA target prediction and functional annotations.

Proper citation: miRDB (RRID:SCR_010848) Copy   

•   Source: SciCrunch Registry

http://home.gwu.edu/~wpeng/Software.htm

A clustering software package for identification of enriched domains from histone modification ChIP-Seq data.

Proper citation: SICER (RRID:SCR_010843) Copy   

•   Source: SciCrunch Registry

http://www.netlab.uky.edu/p/bioinfo/MapSplice

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery.

Proper citation: MapSplice (RRID:SCR_010844) Copy   

•   Source: SciCrunch Registry

http://mocklerlab.org/tools/2

A quality-value guided de novo short read assembler.

Proper citation: QSRA (RRID:SCR_010733) Copy   

•   Source: SciCrunch Registry

http://genetics.cs.ucla.edu/harsh/

Software that provides a method to infer the haplotype using haplotype reference panel and high throughput sequencing data.

Proper citation: HARSH (RRID:SCR_010792) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.jku.at/research/short-IBD/

Software that identifies short identity by descent (IBD) segments that are tagged by rare variants in large sequencing data.

Proper citation: HapFABIA (RRID:SCR_010793) Copy   

•   Source: SciCrunch Registry

http://www.wageningenur.nl/en/show/Pedimap.htm

A software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees.

Proper citation: Pedimap (RRID:SCR_010796) Copy   

•   Source: SciCrunch Registry

http://www.ngsbicocca.org/html/ceqer.html

A graphical, event-driven tool for CNA/AI-coupled analysis of exome sequencing reads.

Proper citation: CEQer (RRID:SCR_010813) Copy   

•   Source: SciCrunch Registry

http://bg.upf.edu/group/projects/oncodrive-fm.php

An approach to uncover driver genes or gene modules.

Proper citation: Oncodrive-fm (RRID:SCR_010781) Copy   

•   Source: SciCrunch Registry

http://www.bcgsc.ca/platform/bioinfo/software/ssake

Software designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets.

Proper citation: SSAKE (RRID:SCR_010753) Copy   

•   Source: SciCrunch Registry

http://www.embl.de/~korbel/CopySeq/

A computational tool that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes.

Proper citation: CopySeq (RRID:SCR_010758) Copy   

•   Source: SciCrunch Registry

https://github.com/ekg/freebayes

A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment.

Proper citation: FreeBayes (RRID:SCR_010761) Copy   

•   Source: SciCrunch Registry