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Software tool for a flow cytometry data analysis for Microsoft Windows enviroment developed by CyFlo Ltd. Has analysis capabilities, such as dot plot, histogram and statistics.
Proper citation: Cyflogic (RRID:SCR_016635) Copy
https://www.ncbi.nlm.nih.gov/sutils/pasc/viridty.cgi
Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database.
Proper citation: PASC (RRID:SCR_016642) Copy
http://home.cc.umanitoba.ca/~frist/Bit/
BIT Core at University of Manitoba, Manitoba, Canada, provides bioinformatics services, resources and collaborations. Support for Genome assembly and annotation, Microarray and Transcriptomics, Systems Biology and Pathway analysis, Databases, Data pipelines, Bioinformatics software, Custom software and programming, Project Wikis, Lab group computer management.
Proper citation: University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility (RRID:SCR_017177) Copy
Community based, biologist friendly web platform for creating and meta analyzing annotated gene expression data compendia., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: OMiCC (RRID:SCR_016604) Copy
https://github.com/wilkinsonlab/epigenomics_pipeline
Software tool as epigenomics analysis pipeline for analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter.
Proper citation: Epigenomics Workflow on Galaxy and Jupyter (RRID:SCR_017544) Copy
Platform to provide tutorials and resources in experimental design and data analysis to researchers interested in using optical mapping data.
Proper citation: OpticalMapping.info (RRID:SCR_017146) Copy
http://www.imgt.org/HighV-QUEST/home.action
Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing.
Proper citation: IMGT HighV-QUEST (RRID:SCR_018196) Copy
https://cran.r-project.org/web/packages/factoextra/index.html
R package from CRAN to extract and visualize the results of multivariate data analysis.
Proper citation: factoextra (RRID:SCR_016692) Copy
https://github.com/neurostuff/NiMARE
Software Python package for coordinate and image based meta analysis of neuroimaging data.
Proper citation: NiMARE (RRID:SCR_017398) Copy
https://www.iconplc.com/innovation/nonmem/
Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions.
Proper citation: NONMEM (RRID:SCR_016986) Copy
Software tool for statistics and data visualization by Red Rock Software, Inc. Provides unparalleled chart selection, data analysis and graph customization capabilities.
Proper citation: Deltagraph (RRID:SCR_018084) Copy
https://www.mirion.com/products/genie-2000-basic-spectroscopy-software
Software tool as comprehensive environment for data acquisition, display and analysis of gamma and alpha spectrometry data.
Proper citation: Genie 2000 Basic (RRID:SCR_021933) Copy
A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene.
Proper citation: ToppCluster (RRID:SCR_001503) Copy
https://github.com/QMICodeBase/TORTOISEV4
An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data.
Proper citation: TORTOISE (RRID:SCR_001645) Copy
Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration.
Proper citation: Gene Weaver (RRID:SCR_003009) Copy
http://seer.cancer.gov/resources/
Portal provides SEER research data and software SEER*Stat and SEER*Prep. SEER incidence and population data associated by age, sex, race, year of diagnosis, and geographic areas can be used to examine stage at diagnosis by race/ethnicity, calculate survival by stage at diagnosis, age at diagnosis, and tumor grade or size, determine trends and incidence rates for various cancer sites over time. SEER releases new research data every Spring based on the previous November’s submission of data.
Proper citation: SEER Datasets and Software (RRID:SCR_003293) Copy
Software library for time-series analysis of data from neuroscience experiments. It contains a core of numerical algorithms for time-series analysis both in the time and spectral domains, a set of container objects to represent time-series, and auxiliary objects that expose a high level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code.
Proper citation: Nitime (RRID:SCR_002504) Copy
https://servicesn.mbi.ucla.edu/SAVES/
Web server for structure validation in homology modeling. Used to validate of obtained crude models. Structure analysis and validation server.
Proper citation: SAVES (RRID:SCR_018219) Copy
Web server for cancer and normal gene expression profiling and interactive analyses. Interactive web server for analyzing RNA sequencing expression data of tumors and normal samples from TCGA and GTEx projects, using standard processing pipeline. Provides customizable functions such as tumor or normal differential expression analysis, profiling according to cancer types or pathological stages, patient survival analysis, similar gene detection, correlation analysis and dimensionality reduction analysis.
Proper citation: Gene Expression Profiling Interactive Analysis (RRID:SCR_018294) Copy
https://github.com/yousra291987/ChiCMaxima
Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling.
Proper citation: ChiCMaxima (RRID:SCR_018178) Copy
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