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https://bellcurve.jp/ex/

Software tool for statistical analysis by BellCurve that adds statistical analysis methods to Excel menu .

Proper citation: Excel Statistics (RRID:SCR_017294) Copy   

•   Source: SciCrunch Registry

http://140.120.197.173/Ecology/prod02.htm

Software tool used to conduct life table analysis focused on development of cohort or population for animal species with two sexes. Parent organization is National Chung Hsing University, Taichung, Taiwan.

Proper citation: TWOSEX-MSChart (RRID:SCR_017298) Copy   

•   Source: SciCrunch Registry

https://syngoportal.org/

Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms.

Proper citation: SynGO (RRID:SCR_017330) Copy   

•   Source: SciCrunch Registry

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

Software R package for phylogenetic reconstruction and analysis. Used for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks.

Proper citation: Phangorn (RRID:SCR_017302) Copy   

•   Source: SciCrunch Registry

https://beast.community/tempest

Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019.

Proper citation: TempEst (RRID:SCR_017304) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/morpheus/

Software tool for versatile matrix visualization and analysis. Program to generate heatmaps from input data. JavaScript matrix visualization and analysis.

Proper citation: Morpheus by Broad Institute (RRID:SCR_017386) Copy   

•   Source: SciCrunch Registry

https://www.qiagenbioinformatics.com/products/clc-genomics-server/

Commercially available software tool for high throughput sequencing analysis, designed for use on central compute cluster or server. Can handle data volumes beyond capacity of desktop systems and manages submission of many jobs via its own queuing system or through submission of jobs to third party grid scheduler.

Proper citation: CLC Genomics Server (RRID:SCR_017396) Copy   

•   Source: SciCrunch Registry

http://carolina.imis.athena-innovation.gr/mirextra/

Software tool for analysis of expression data for microRNA function.

Proper citation: DIANA-mirExTra (RRID:SCR_017498) Copy   

•   Source: SciCrunch Registry

http://neurocics.udd.cl/LANtoolbox.html

Software toolbox for neuroscientist data (EEG and reaction time for time being). Used to create shared language among different algorithms and softwares in this field (e.g. Fieldtrip, Eeglab, Chronux, Brainstorm, etc), in order to facilitate implementation of experimental analysis by users. Code and scripts for EEG analysis for MATLAB.

Proper citation: LAN toolbox (RRID:SCR_017629) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/TCGAbiolinks/

Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R.

Proper citation: TCGAbiolinks (RRID:SCR_017683) Copy   

•   Source: SciCrunch Registry

https://github.com/gdancik/shinyGEO

Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets.

Proper citation: shinyGEO (RRID:SCR_017605) Copy   

•   Source: SciCrunch Registry

http://www.mysamplesize.com

Software tool for experimental design, sample size determination and analysis by Tempest Technologies.

Proper citation: mysamplesize (RRID:SCR_017575) Copy   

•   Source: SciCrunch Registry

http://refgenie.databio.org

Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis.

Proper citation: refgenie (RRID:SCR_017574) Copy   

•   Source: SciCrunch Registry

https://leora-software.com/products/poloplusonline

Software to perform Probit and Logit analsis with grouped data. Original Polo Software available through USB Drive. Able to work on all versions of Windows as all files are kept on USB.

Proper citation: PoloPlus USB Drive software (RRID:SCR_017614) Copy   

•   Source: SciCrunch Registry

http://statpackets.org/

Standardized method to export statistical data, associated with KOMP project. Standard way to keep data and results of analyzing that data together.

Proper citation: StatPackets (RRID:SCR_017613) Copy   

•   Source: SciCrunch Registry

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

Software package provides interface from R to JAGS library for Bayesian data analysis. Program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.

Proper citation: rjags (RRID:SCR_017573) Copy   

•   Source: SciCrunch Registry

https://github.com/padster/pyDynamo/

Software tool for neuron timelapse reconstruction, registration and analysis for Dynamic Morphometrics.

Proper citation: Dynamo (RRID:SCR_017541) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/wormlab

Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays.

Proper citation: Worm Lab (RRID:SCR_017669) Copy   

•   Source: SciCrunch Registry

https://github.com/LaBiOS/Transcriptive

Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results.

Proper citation: Transcriptive (RRID:SCR_017545) Copy   

•   Source: SciCrunch Registry

http://www.milesculabs.org/QuB.html

Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: QuB (RRID:SCR_018076) Copy   

•   Source: SciCrunch Registry