Tools   Select Another Resource Report Type

https://bitbucket.org/biobakery/biobakery/wiki/Home

Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: biobakery (RRID:SCR_016596) Copy   

•   Source: SciCrunch Registry

https://github.com/vaklip/rsfmri_fconn

Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity.

Proper citation: rsfMRI_fconn calculation (RRID:SCR_016591) Copy   

•   Source: SciCrunch Registry

http://phenomenal-h2020.eu/

Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics.

Proper citation: PhenoMeNal (RRID:SCR_016605) Copy   

•   Source: SciCrunch Registry

https://niaid.github.io/spice/

Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically.

Proper citation: SPICE (RRID:SCR_016603) Copy   

•   Source: SciCrunch Registry

https://joinsolver.niaid.nih.gov

Software tool to analyze human immunoglobulin V(D)J recombination and performing Ig nucleotide and amino acid alignment, as well as extensive mutation and Complementarity Determining Region 3 (CDR3H) analysis.

Proper citation: JOINSOLVER (RRID:SCR_016619) Copy   

•   Source: SciCrunch Registry

https://www.niaid.nih.gov/research/simmune-project

Software package to define the interactions between individual molecules in a large network or the behaviors of cells in response to external signals. It consists of three components: Modeler, Cell Designer and Simulator.

Proper citation: Simmune (RRID:SCR_016618) Copy   

•   Source: SciCrunch Registry

https://github.com/CPernet/spmup/

Software Project Management (SPM) tools which contain a collection of functions that can be used at different stage of a standard massive univariate fMRI data analysis. Used to improve mass univariate analysis.

Proper citation: SPM U+ (RRID:SCR_016743) Copy   

•   Source: SciCrunch Registry

https://www.metaboanalyst.ca/

Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification.

Proper citation: MetaboAnalyst (RRID:SCR_015539) Copy   

•   Source: SciCrunch Registry

https://CalRapp.org

A Web-based Analysis Tool for Indirect Calorimetry Experiments which measure physiological energy balance. It is a web application for indirect calorimetry analysis which generates customizable time, bar and regression plots for calorimetry data using two-, three-, and four-group templates.

Proper citation: CalR (RRID:SCR_015849) Copy   

•   Source: SciCrunch Registry

https://www.biacore.com/lifesciences/service/downloads/software_licenses/biaevaluation/

Analysis software for life science data. This software package is for presentation and evaluation of sensorgram data from real-time BIA analyses.

Proper citation: BIAevaluation Software (RRID:SCR_015936) Copy   

•   Source: SciCrunch Registry

https://github.com/jdiedrichsen/pcm_toolbox

Software for a Bayesian approach for evaluating representational models that specify how complex patterns of neural activity relate to visual stimuli, motor actions, or abstract thoughts. PCM evaluates the ability of models to predict novel brain activity patterns and integrates over all possible activity profiles and computes the marginal likelihood of the data under the activity profile distribution specified by the representational model.

Proper citation: Pattern Component Modelling Toolbox (RRID:SCR_015891) Copy   

•   Source: SciCrunch Registry

https://anvio.org

Open source software analysis and visualization platform for microbial omics including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in integrated fashion through extensive interactive visualization capabilities.

Proper citation: Anvi'o (RRID:SCR_021802) Copy   

•   Source: SciCrunch Registry

http://bmsr.usc.edu/software/lysis/

Interactive software of a set of modular programs (each performing a specific task) that provide an integrated computing environment for data analysis and system modeling. Unique capabilities of LYSIS include input-output nonlinear system modeling and the novel methodology of Principal Dynamic Modes (PDMs). LYSIS is currently available in two versions: one for LYSIS 7.1 Windows and one for LYSIS 7.2 Matlab. Early versions are also available for UNIX environments, distributed as source code that can be compiled for each UNIX implementation (e.g., Solaris, HPUX, Linux). Specific features of LYSIS that cannot be found in commercially available packages include the efficient kernel estimation using Laguerre expansions and the use of Principal Dynamic Modes (PDMs). These enable input-output modeling of dynamic nonlinear systems with relatively short data-records (even in the presence of considerable noise). System Requirements * Operating System ** Windows XP/Vista/7 ** Sun/Unix: Solaris 2.x

Proper citation: LYSIS (RRID:SCR_001385) Copy   

•   Source: SciCrunch Registry

http://www.neuroexplorer.com/

Data analysis software for neurophysiology with a multitude of features, including: * Import of native data files created by many popular data acquisition systems * All standard histogram and raster analyses * Shift predictors in crosscorrelograms and color markers in perievent rasters * Joint PSTH, burst analysis and many more analyses of timestamped data * Spectral analysis of spike and continuous data * 3D data view and animation * Fully customizable WYSIWYG graphics * Custom analysis and batch mode processing with internal scripting language * Direct data link to Matlab and Excel * Statistical tests via direct link to R-project

Proper citation: NeuroExplorer (RRID:SCR_001818) Copy   

•   Source: SciCrunch Registry

http://www.neuronland.net/NLMorphologyConverter/NLMorphologyConverter.html

NLMorphologyConverter is a simple command-line program for converting between the various neuron morphology data formats which are used to describe the three-dimensional physical branching structure of biological neurons. The aim is to provide coverage of all formats, old and new, in which data is available online, and/or which are supported by free and commercial software packages (e.g. software for neuron reconstruction, generation, simulation, visualization, and analysis of neuron morphology). Permission is granted for this software to be freely copied. Main Features Currently 21 different morphology file formats fully or partially supported. Automatic detection of input file format. Faithful reproduction of output file formatting. Many command line options for manipulating the imported data Intensively tested using over 10000 publicly available morphology data files. Sponsors. This software is supported by NeuronLand.

Proper citation: Neuronland: NLMorphologyConverter (RRID:SCR_001817) Copy   

•   Source: SciCrunch Registry

https://www.libreoffice.org/

Open source software application with data analysis tools and spreadsheet templates used to manage, process and visualize data. LibreOffice Calc is spreadsheet component of LibreOffice software package developed by Document Foundation.

Proper citation: LibreOfficeCalc (RRID:SCR_018013) Copy   

•   Source: SciCrunch Registry

https://www.bio-rad.com/en-us/product/bio-plex-200-systems?ID=715b85f1-6a4e-41b3-b5d9-80202d779e13

Suspension array system which offers protein and nucleic acid researchers multiplex assay solution permiting analysis of up to 100 biomolecules in single sample.

Proper citation: Bio-Rad: Bio-Plex 200 System (RRID:SCR_018026) Copy   

•   Source: SciCrunch Registry

https://pedsresearch.org/uploads/pages/img/LuminexManual_LX100.pdf

Flow cytometry analyzer system for individual labs that performs up to 100 different tests in single reaction volume and can use either magnetic beads or plain polystyrene beads.

Proper citation: Luminex: 100 Flow Cytometry Analyzer System (RRID:SCR_018025) Copy   

•   Source: SciCrunch Registry

https://github.com/shanemomara/omaraneurolab/tree/master/NeuroChaT

Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories.

Proper citation: NeuroChaT (RRID:SCR_018020) Copy   

•   Source: SciCrunch Registry

https://github.com/hariszaf/pema

Software as flexible pipeline for environmental DNA metabarcoding analysis of 16S/18S rRNA, ITS and COI marker genes. Performs reads’ pre-processing, clustering to (M)OTUs and taxonomy assignment for 16S rRNA and COI marker gene data. Allows users to explore alternative algorithms for specific steps of pipeline without need of complete re-execution.

Proper citation: PEMA (RRID:SCR_017676) Copy   

•   Source: SciCrunch Registry