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https://www.flimfit.org/

Software package for quantitative analysis of large Fluorescence Lifetime Imaging Microscopy (FLIM) data, including global analysis. It is able to routinely analyse multi-well plate FLIM datasets on conventional PC workstations in a reasonable time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FLIMfit (RRID:SCR_016298) Copy   

•   Source: SciCrunch Registry

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

Software general R package providing standard methods for meta analysis.

Proper citation: meta (RRID:SCR_019055) Copy   

•   Source: SciCrunch Registry

https://github.com/sqjin/CellChat

Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets.

Proper citation: CellChat (RRID:SCR_021946) Copy   

•   Source: SciCrunch Registry

http://www.ntnu.edu/hunt

International biobank storing whole blood and DNA from 200,000 individuals, serum and plasma samples from more than 100,000 individuals as well as urine, RNA tubes, cells, buffy coat and Na-heparin tubes for environmental analysis for as many as 50,000 individuals. All bio-specimens from the HUNT surveys are collected, processed and stored at the HUNT Biobank in Levanger. The National CONOR Biobank is located on the same site, where it serves as a central research repository for DNA samples from all the largest Norwegian health surveys. These make up the Cohorts of Norway (CONOR), which include samples from more than 200,000 individuals. * HUNT 1 was carried out in 1984-1986 to establish the health history of 75,000 people. * HUNT 2, carried out in 1995-1997, focused on the evolution of the health history of 74,000 people. This included blood sample collection from 65,000 people. The data that accompany biospecimens in the biobank are stored in secured computer systems that run complex database management and analysis software. * HUNT 3 was completed in June 2008. 93,210 people were invited to participate in the study, and as of the 6th of June, 2008, 48,289 people participated (52% participation rate). The data, collected by means of questionnaires, interviews, clinical examinations and collection of blood and urine samples, will be ready for analysis in January 2009. * Young-HUNT is the adolescent part of HUNT including participants aged 13-19 years. Young-HUNT1 (1995-97) was conducted as part of HUNT2, 9141 adolescents participated (90% response rate). Young-HUNT2 (2000-01) was a follow-up study of Young-HUNT1, 2400 students participated in both studies (77% of the invited). Young-HUNT3 (2006-08) was a new cross-sectional study as part of HUNT3. This time 8677 adolescents participated (87% response rate). Data collection included self-reported questionnaires, structured interviews, clinical measurements and, in Young-HUNT3, buccal smears. All institutions with research expertise can apply for access to analyze HUNT data. Projects must have recommendations from The Regional Committee for Medical Research in Norway (REK) and be registered with The Norwegian Social Science Data Services (NSD).

Proper citation: Hunt Biobank (RRID:SCR_010626) Copy   

•   Source: SciCrunch Registry

https://github.com/facebook/prophet

Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton.

Proper citation: Prophet (RRID:SCR_017083) Copy   

•   Source: SciCrunch Registry

http://regent.qc.ca/assets/winrhizo_software.html

Software toolbox for image analysis by Regent Instruments Inc. Used for root measurement in different forms like morphology, topology, architecture and color analyses. Automatically or interactively analyses washed roots.

Proper citation: WinRHIZO (RRID:SCR_017120) Copy   

•   Source: SciCrunch Registry

https://github.com/neuropoly/qMRLab

Software for quantitative MR image analysis, simulation, and protocol optimization. It aims to provide the community with a tool for data fitting, plotting, simulation and protocol optimization for a variety of different quantitative models.

Proper citation: qMRLab (RRID:SCR_016256) Copy   

•   Source: SciCrunch Registry

http://lincs.hms.harvard.edu/

Center that is part of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program. Its goals are to collect and disseminate data and analytical tools needed to understand how human cells respond to perturbation by drugs, the environment, and mutation.

Proper citation: HMS LINCS Center (RRID:SCR_016370) Copy   

•   Source: SciCrunch Registry

https://www.med.upenn.edu/cbica/captk/

Software platform for analysis of radiographic cancer images. Used as quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.

Proper citation: Cancer Imaging Phenomics Toolkit (RRID:SCR_017323) Copy   

•   Source: SciCrunch Registry

http://hmri.info

Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.

Proper citation: hMRI-toolbox (RRID:SCR_017682) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/stereo-investigator-cleared-tissue-edition

Software tool for unbiased stereology to be used on cleared tissue. Used to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes. Includes number, length, area and volume analyses.

Proper citation: Stereo Investigator - Cleared Tissue Edition (RRID:SCR_017668) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://toppcluster.cchmc.org/

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   

•   Source: SciCrunch Registry

http://www.GeneWeaver.org

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://nipy.org/nitime/

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   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/geo/

Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.

Proper citation: Gene Expression Omnibus (GEO) (RRID:SCR_005012) Copy   

•   Source: SciCrunch Registry

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https://github.com/spm

Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.

Proper citation: SPM (RRID:SCR_007037) Copy   

•   Source: SciCrunch Registry

http://vortex.cs.wayne.edu/projects.htm#Onto-Compare

Microarrays are at the center of a revolution in biotechnology, allowing researchers to screen tens of thousands of genes simultaneously. Typically, they have been used in exploratory research to help formulate hypotheses. In most cases, this phase is followed by a more focused, hypothesis driven stage in which certain specific biological processes and pathways are thought to be involved. Since a single biological process can still involve hundreds of genes, microarrays are still the preferred approach as proven by the availability of focused arrays from several manufacturers. Since focused arrays from different manufacturers use different sets of genes, each array will represent any given regulatory pathway to a different extent. We argue that a functional analysis of the arrays available should be the most important criterion used in the array selection. We developed Onto-Compare as a database that can provide this functionality, based on the GO nomenclature. Compare commercially available microarrays based on GO. User account required. Platform: Online tool

Proper citation: Onto-Compare (RRID:SCR_005669) Copy   

•   Source: SciCrunch Registry