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http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/

Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality.

Proper citation: Cufflinks (RRID:SCR_014597) Copy   

•   Source: SciCrunch Registry

http://cyberinncorp.com/SigmaGel.htm

Gel analysis software which can be used on a PC with TWAIN-compatible scanners without specialty equipment. Users scan or load an image which can then be calibrated. SigmaGel allows users to make lane measurements, spot measurements, and molecular weight measurements. After data analysis was completed, users can print or copy and paste data and images.

Proper citation: SigmaGel Software (RRID:SCR_014598) Copy   

•   Source: SciCrunch Registry

http://www.cbn-atl.org/research/stopwatch.shtml

A software which tracks the number of occurrences and duration of up to 16 defined events. The user can group events together so that turning on one event in a group will automatically turn off other active events in the group. Sessions can end after a fixed length of time, or the sessions can be ended manually, At the end of the session, the data can be saved in a comma-delimited file which can be easily imported into a spreadsheet application.

Proper citation: Stopwatch+ (RRID:SCR_014591) Copy   

•   Source: SciCrunch Registry

http://statplus-mac.en.softonic.com/mac

A statistical data analysis tool that works with Microsoft Excel and is designed especially for use in IOS systems. Tutorials and examples are provided within the program.

Proper citation: StatPlus Mac (RRID:SCR_014635) Copy   

•   Source: SciCrunch Registry

http://www6.appliedbiosystems.com/support/software/copycaller/CopyCallerUserGuide.pdf

A software for analyzing real-time PCR data and quantifying DNA targets. It can perform copy number analysis, report confidence in copy number, display data in table and graphic format, change analysis parameters, and view data analysis information for multiple experiments at once.

Proper citation: CopyCaller (RRID:SCR_014486) Copy   

•   Source: SciCrunch Registry

https://www.minitab.com/en-us/products/minitab/

A statistical software package that allows the user to import data, create graphs, and perform statistical analysis. It can perform basic statistical tests like descriptive statistics, hypothesis tests, confidence intervals, and normality tests as well as regression and ANOVA and quality assessment.

Proper citation: Minitab (RRID:SCR_014483) Copy   

•   Source: SciCrunch Registry

https://www.bdbiosciences.com/documents/15_cellquest_prosoft_analysis.pdf

A software for acquiring and analyzing flow cytometry data. The user can create plots with elements like regions, gates, statistics, markers, and annotated text. The software can also be used for batch analysis or quality control of analysis. Results can be exported and saved., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BD CellQuest Pro (RRID:SCR_014489) Copy   

•   Source: SciCrunch Registry

http://www.evolution.rdg.ac.uk/BayesTraits.html

A computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. It incorporates earlier programs including Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a discrete number of states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, ancestral states and correlations among pairs of traits., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BayesTraits (RRID:SCR_014487) Copy   

•   Source: SciCrunch Registry

http://www.scied.com/pr_cmbas.htm

A software system to assist with cloning simulation, enzyme operations, and graphic map drawing. Clone Manager can also be used as a way to view or edit sequence files, find open reading frames, translate genes, or find genes or text in files. Clone Manager Professional is an upgraded version of Clone Manager Basic., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Clone Manager Software (RRID:SCR_014521) Copy   

•   Source: SciCrunch Registry

http://aleasol.ch/cms/index.php/clickjoint.en.html

A software for analyzing animal movement on videos and images. The user can define the animal's joints so the software can analyze using a tracking algorithm.

Proper citation: Clickjoint (RRID:SCR_014482) Copy   

•   Source: SciCrunch Registry

http://hmpdacc.org/resources/tools_protocols.php

A tool used to screen for core gene sets as an indicator of completeness of draft genomes. The download includes a Perl script and required archaeal and bacterial core genes fasta and cluster files.

Proper citation: Core Gene Evaluation Script (RRID:SCR_014604) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/invue/

An API and software suite for large scale data visualization and analysis.

Proper citation: inVUE (RRID:SCR_014608) Copy   

•   Source: SciCrunch Registry

http://rast.nmpdr.org

A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes.

Proper citation: RAST Server (RRID:SCR_014606) Copy   

•   Source: SciCrunch Registry

http://www.med-associates.com/product-category/video-software/

Automation software used to analyze fear behavior in rodents. Freezing is represented in the data file in several different ways, including the total time the subject spends motionless during the session, the percent of time motionless, the number of freezing episodes or occurrences, or as an average index of motion.

Proper citation: Med Associates Video Freeze Software (RRID:SCR_014574) Copy   

•   Source: SciCrunch Registry

https://www.deshawresearch.com/resources_desmond.html

Software designed to perform high-speed molecular dynamic simulations of biological systems on conventional commodity clusters, supercomputers and GPUs. This code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms with a large number of processors. It can be used with a single computer.

Proper citation: Desmond (RRID:SCR_014575) Copy   

•   Source: SciCrunch Registry

http://www.brainsimagebank.ac.uk

A searchable collection of anonymised images and associated clinical data. It includes normal individuals at all ages (from prenatal to old age). The image bank contains integrated data sets already collected as part of research studies which include control subjects. New data is added as they become available.

Proper citation: BRAINS Imagebank (RRID:SCR_014576) Copy   

•   Source: SciCrunch Registry

https://www.licor.com/bio/products/imaging_systems/odyssey/

A data analysis software developed to simplify and record data from fluorescent related assays such as Western Blots, EMSAs, and Western Assays. This software will consolidate all of the resulting data into one easy-to-track image, and thus removes the need for multiple exposures, as well as standardizing the resulting fluorescent bands without image saturation, blowout, or removed sensitivity. Odyssey CLx is capable of scanning multiple mini-blots, microplates, or slides at the same time.

Proper citation: Odyssey CLx (RRID:SCR_014579) Copy   

•   Source: SciCrunch Registry

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

An R-package which uses Dirichlet-Multinomial distribution to perform formal hypothesis testing on the species abundance distribution of human microbiome data, and to calculate power and sample size requirements for human microbiome experiments.

Proper citation: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP (RRID:SCR_014612) Copy   

•   Source: SciCrunch Registry

http://biocore.github.io/SitePainter/

An interactive data visualization tool which allows users to create and upload pictures of their study site, load diversity analyses, and display both diversity and taxonomy results in a spatial context.

Proper citation: SitePainter (RRID:SCR_014618) Copy   

•   Source: SciCrunch Registry

http://aem.asm.org/content/71/12/8228.full

THIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. A suite of tools for the comparison of microbial communities using phylogenetic information. It takes as input a single phylogenetic tree that contains sequences derived from at least two different environmental samples and a file describing which sequences came from which sample.

Proper citation: Unifrac (RRID:SCR_014616) Copy   

•   Source: SciCrunch Registry