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http://www.genomics.agilent.com/en/Microarray-Data-Analysis-Software/GeneSpring-GX/?cid=AG-PT-130&tabId=AG-PR-1061

Powerful, accessible statistical tools for fast visualization and analysis of microarrays - expression arrays, miRNA, exon arrays and genomics copy number data.

Proper citation: GeneSpring GX (RRID:SCR_010972) Copy   

•   Source: SciCrunch Registry

http://www.rhino3d.com/features

3D modeling software used to create, edit, analyze, document, render, animate, and translate surfaces, solids, point clouds, and polygon meshes. It can also be used to analyze and manufacture a variety of products.

Proper citation: Rhinoceros (RRID:SCR_014339) Copy   

•   Source: SciCrunch Registry

https://web.stanford.edu/group/pritchardlab/structure.html

Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms.

Proper citation: STRUCTURE (RRID:SCR_017637) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/argus/

Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior.

Proper citation: Argus (RRID:SCR_021585) Copy   

•   Source: SciCrunch Registry

https://www.syngene.com/software/genetools-automatic-image-analysis/

Software package includes comprehensive tools to provide full range of analysis for applications including chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging and colony counting.

Proper citation: GeneTools (RRID:SCR_022505) Copy   

•   Source: SciCrunch Registry

http://www.perkinelmer.com/pages/020/cellularimaging/products/openlab.xhtml

A software package for performing 2D microscope image processing and integrating and controlling a diverse array of instrumentation in a laboratory environment. The software suite has four basic areas of operation acquisition, image presentation, and storage, analysis, and automation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Openlab (RRID:SCR_012158) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=cluster

Software R package. Methods for Cluster analysis. Performs variety of types of cluster analysis and other types of processing on large microarray datasets.

Proper citation: Cluster (RRID:SCR_013505) Copy   

•   Source: SciCrunch Registry

http://www.inteligand.com/ligandscout/

Software that takes a macromolecular structure containing a bound ligand and identifies the key features on the ligand which are interacting with points on a protein. Its features include: automatic interpretation of PDB ligands using geometry, dictionaries and rule; advanced handling of co-factors, ions, water molecules and covalently bound ligands; pharmacophore export to Catalyst(tm), MOE(tm) and PHASE(tm) for virtual screening; and the ability to treat co-factors and water molecules as part of the ligand or part of the macromolecule.

Proper citation: LigandScout (RRID:SCR_014889) Copy   

•   Source: SciCrunch Registry

http://www.wavefun.com/

Software program for determining molecular structure and calculating chemical properties. It has a graphical interface and accurate computational models that are compatible with the iPad, iPhone and iPod Touch. When combined with the Spartan'16 Parallel Suite, this enables the first fully-functional open-ended molecular modeling environment on popular mobile technology.

Proper citation: SPARTAN (RRID:SCR_014901) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/4363991

Software that allows users to manually or automatically design custom primers and probes for gene quantitation and allelic discrimination (SNP) real-time PCR applications. It supports assays based on TaqMan and SYBR Green I dye chemistries.

Proper citation: Primer Express (RRID:SCR_014326) Copy   

•   Source: SciCrunch Registry

http://www.hkl-xray.com/hkl-2000

Software package for structural determination and other functions in the field of structural biology. Its programs can perform strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, and other functions.

Proper citation: HKL-2000 (RRID:SCR_015547) Copy   

•   Source: SciCrunch Registry

https://www.sqlite.org/index.html

Relational database management system contained in C library. SQLite is not client server database engine but it is embedded into the end program.

Proper citation: SQLite (RRID:SCR_017672) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=survival

Software R package contains core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

Proper citation: survival (RRID:SCR_021137) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=caret

Software R package provides misc functions for training and plotting classification and regression models.Contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality.

Proper citation: caret (RRID:SCR_021138) Copy   

•   Source: SciCrunch Registry

http://mutationassessor.org/

A web server that predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. The method has been validated on a large set (51k) of disease associated (OMIM) and polymorphic variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MutationAssessor (RRID:SCR_005762) Copy   

•   Source: SciCrunch Registry

http://bioapps.rit.albany.edu/MITOPRED/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It predicts nuclear-encoded mitochondrial proteins from all eukaryotic species including plants. Prediction is based on the occurrence patterns of Pfam domains (version 16.0) in different cellular locations, amino acid composition and pI value differences between mitochondrial and non-mitochondrial locations. Additionally, you may download MITOPRED predictions for complete proteomes. Re-calculated predictions are instantly accessible for proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Homo sapiens, Mus musculus and Arabidopsis species as well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases. Queries, at different confidence levels, can be made through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a local file with such accession numbers; (iii) entering protein sequences; (iv) uploading a local file containing protein sequences in FASTA format. The Mitopred algorithm works based on the differences in the Pfam domain occurrence patters and amino acid composition differences in different cellular compartments. Location specific Pfam domains have been determined from the entire eukaryotic set of Swissprot database. Similarly, differences in the amino acid composition between mitochondrial and non-mitochondrial sequences were pre-calculated. This information is used to calculate location-specific amino acid weights that are used to calculate amino acid score. Similarly, pI average values of the N-terminal 25 residues in different cellular location were also determined. This knowledge-base is accessed by the program during execution.

Proper citation: mitopred (RRID:SCR_006135) Copy   

•   Source: SciCrunch Registry

http://gbrowse.org/

A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions.

Proper citation: GBrowse (RRID:SCR_006829) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/

Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.

Proper citation: Bioconductor (RRID:SCR_006442) Copy   

•   Source: SciCrunch Registry

http://www.helsinki.fi/~tsjuntun/linkage/analyze/

A set of useful accessory programs to the LINKAGE package. It simplifies the performance of a large array of parametric and nonparametric tests for linkage and association on data entered in LINKAGE format pedigree and parameter files. (entry from Genetic Analysis Software)

Proper citation: ANALYZE (RRID:SCR_009120) Copy   

•   Source: SciCrunch Registry

http://hydra.usc.edu/GxE

Software program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs. Quanto is a 32-bit Windows application requiring Windows 95, 98, NT, 2000, ME or XP to run. The graphical user interface allows th e user to easily change the model and view the results without having to edit an input file and rerun the program for every model. The results of a session are stored to a log file. This log can be printed or saved to a file for reviewing at a later date. An option is included to create a text file of the log that can be imported into other documents. (entry from Genetic Analysis Software)

Proper citation: QUANTO (RRID:SCR_009084) Copy   

•   Source: SciCrunch Registry