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http://apps.cytoscape.org/apps/pepper

A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...).

Proper citation: PEPPER (RRID:SCR_000431) Copy   

•   Source: SciCrunch Registry

https://as.nyu.edu/research-centers/cbi/resources/Software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software which converts DICOM images to NIfTI format.

Proper citation: dinifti (RRID:SCR_000303) Copy   

•   Source: SciCrunch Registry

http://gusevlab.org/projects/germline/

Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GERMLINE (RRID:SCR_001720) Copy   

•   Source: SciCrunch Registry

http://gmt.genome.wustl.edu/packages/breakdancer/

A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software)

Proper citation: BREAKDANCER (RRID:SCR_001799) Copy   

•   Source: SciCrunch Registry

http://haplopainter.sourceforge.net/

A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software)

Proper citation: HAPLOPAINTER (RRID:SCR_001710) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/pedhunter.html

Software package that facilitates creation and verification of pedigrees within large genealogies. The pedigrees are produced as files in LINKAGE format ready for linkage analysis and for drawing with a variety of drawing programs, such as PEDDRAW and cranefoot.

Proper citation: PEDHUNTER (RRID:SCR_002031) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/a/brain.org.au/ctp/

Software package with functions that will help researchers plan how many subjects per group need to be included in an MRI-based cortical thickness study to ensure a thickness difference is detected. The package requires cortical thickness mapping and co-registration to be carried out using Freesurfer. The power analyses are implemented in the R software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: cortex (RRID:SCR_002467) Copy   

•   Source: SciCrunch Registry

http://people.virginia.edu/~wc9c/TDTPC/Download.htm

Software program to compute the statistical power of the Transmission/Disequilibrium Test (TDT) analytically, based on the most accurate asymptotic algorithms up to date, and is applicable in very general situations, where different parental disease status, multiple children, mixed family type and recombination events are considered. Routine algorithms for Monte Carlo simulations with significant improvements are also implemented in this program. (entry from Genetic Analysis Software)

Proper citation: TDT-PC (RRID:SCR_001116) Copy   

•   Source: SciCrunch Registry

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https://cran.r-project.org/web/packages/adegenet/index.html

Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)

Proper citation: ADEGENET (RRID:SCR_000825) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/browning/beagle/beagle.html

Software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can * phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. * infer sporadic missing genotype data. * impute ungenotyped markers that have been genotyped in a reference panel. * perform single marker and haplotypic association analysis. * detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals. Beagle can also be used in conjunction with PRESTO, a program for fast and flexible permutation testing. PRESTO can compute empirical distributions of order statistics, analyze stratified data, and determine significance levels for one-stage and two-stage genetic association studies. BEAGLE is written in Java and runs on any computing platform with a Java version 1.6 interpreter (e.g. Windows, Unix, Linux, Solaris, Mac).

Proper citation: BEAGLE (RRID:SCR_001789) Copy   

•   Source: SciCrunch Registry

http://openmeeg.gforge.inria.fr

A C++ package for low-frequency bio-electromagnetism solving forward problems in the field of EEG and MEG with very high accuracy.

Proper citation: OpenMEEG (RRID:SCR_002510) Copy   

•   Source: SciCrunch Registry

http://animalgene.umn.edu/locusmap/index.html

Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software)

Proper citation: LOCUSMAP (RRID:SCR_000840) Copy   

•   Source: SciCrunch Registry

https://www.jurgott.org/linkage/LinkagePC.html

Standard software package for genetic linkage called LINKAGE. Genetic linkage analysis is statistical technique used to map genes and find approximate location of disease genes.

Proper citation: LINKAGE (RRID:SCR_007033) Copy   

•   Source: SciCrunch Registry

http://www.rightfield.org.uk/

An open-source tool for adding ontology term selection to Excel spreadsheets. It is used by a "Template Creator" to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection. RightField is a standalone Java application which uses Apache-POI for interacting with Microsoft documents. It enables users to import Excel spreadsheets, or generate new ones from scratch. Ontologies can either be imported from their local file systems, or from the BioPortal ontology repository. Individual cells, or whole columns or rows can be marked with the required ranges of ontology terms and an individual spreadsheet can be annotated with terms from multiple ontologies.

Proper citation: RightField (RRID:SCR_002649) Copy   

•   Source: SciCrunch Registry

http://www.altanalyze.org/

Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph.

Proper citation: AltAnalyze - Alternative Splicing Analysis Tool (RRID:SCR_002951) Copy   

•   Source: SciCrunch Registry

http://compgen.rutgers.edu/multimap.shtml

Software program for automated construction of genetic maps (entry from Genetic Analysis Software)

Proper citation: MULTIMAP (RRID:SCR_007168) Copy   

•   Source: SciCrunch Registry

http://od1n.sourceforge.net

A C++ software framework to develop, simulate and run magnetic resonance sequences on different platforms.

Proper citation: Object-Oriented Development Interface for NMR (RRID:SCR_005974) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ua.pt/coeus/

A semantic web-powered knowledge management framework, aiming at a streamlined application development cycle and following a semantic web in a box approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. It is targeted at rapid application deployment of new applications in any research field, supported by a comprehensive integration engine and an advanced data distribution API.

Proper citation: COEUS (RRID:SCR_006287) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/folders/melanie/haploclusters.html

Software program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. (entry from Genetic Analysis Software)

Proper citation: HAPLOCLUSTERS (RRID:SCR_007439) Copy   

•   Source: SciCrunch Registry

http://aspex.sourceforge.net/

A set of programs for performing multipoint exclusion mapping of affected sibling pair data for discrete traits. (entry from Genetic Analysis Software)

Proper citation: ASPEX (RRID:SCR_008414) Copy   

•   Source: SciCrunch Registry