Tools   Select Another Resource Report Type

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://bioconductor.org/packages/release/bioc/html/riboSeqR.html

Software tool for analysis of sequencing data from ribosome profiling experiments. Used for plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.

Proper citation: riboSeqR (RRID:SCR_016947) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Rsubread.html

Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.

Proper citation: Rsubread (RRID:SCR_016945) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/scran.html

Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection.

Proper citation: scran (RRID:SCR_016944) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html

Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots.

Proper citation: ConsensusClusterPlus (RRID:SCR_016954) Copy   

•   Source: SciCrunch Registry

https://github.com/maypoleflyn/BSATOS

Software tools for next generation sequencing based bulked segregation analysis for outbreeding species including fruit trees such as apple or cirtus. Used to improve gene mapping efficiency of next generation sequencing based segregant analysis in outbreeding species and realize rapid candidate gene mining based on multi-omics data.

Proper citation: Bulked segregation analysis tools for outbreeding species (RRID:SCR_017009) Copy   

•   Source: SciCrunch Registry

https://github.com/fyz11/MOSES

Computational Python library for the motion analysis of biological single-cell and collective motion for high content screens. Framework to quantify and discover cellular motion phenotypes.

Proper citation: Motion Sensing Superpixels (MOSES) (RRID:SCR_016839) Copy   

•   Source: SciCrunch Registry

http://www.perkinelmer.co.uk/lab-solutions/resources/PDFs/LST/Specifications/SPC_CyclonePlusStoragePhosphor.pdf

Software package for image acquisition, analysis, display, and archiving. Used to quantify the autoradiography data from Cyclone apparatus from Perkin Elmer.

Proper citation: OptiQuant Software (RRID:SCR_016769) Copy   

•   Source: SciCrunch Registry

http://mixomics.org/access/

Software R package of multivariate methods for the exploration and integration of biological datasets with a focus on variable selection. Used to analyse data from high throughput sequencing technologies and spectral imaging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: mixOmics (RRID:SCR_016889) Copy   

•   Source: SciCrunch Registry

https://biii.eu/

Web platform for bio image analysis. Used to share knowledge between the different communities, to help biologists to find any tool or workflow available for a particular image analysis problem and to find the adequate image processing wording, to help software and algorithm developers to find missing tools (or components), and to help bioimage analyst to identify and edit workflows.

Proper citation: BISE (RRID:SCR_016774) Copy   

•   Source: SciCrunch Registry

https://uk.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image

Matlab based scripts for load, save, make, reslice, view and edit both Neuroimaging Informatics Technology Initiative (NIfTI) and ANALYZE data on any platform.

Proper citation: Tools for NIfTI and ANALYZE image (RRID:SCR_016895) Copy   

•   Source: SciCrunch Registry

https://github.com/SofieVG/FlowSOM

Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise.

Proper citation: FlowSOM (RRID:SCR_016899) Copy   

•   Source: SciCrunch Registry

https://github.com/gelles-brandeis/CoSMoS_Analysis

Software tools for analyzing co-localization single-molecule spectroscopy image data.

Proper citation: CoSMoS_Analysis (RRID:SCR_016896) Copy   

•   Source: SciCrunch Registry

https://github.com/ICB-DCM/PESTO

Software customizable toolbox for parameter estimation in MathWorks MATLAB. Offers scalable algorithms for optimization, uncertainty and identifiability analysis which do not depend on any problem-specific assumptions.

Proper citation: PESTO (RRID:SCR_016891) Copy   

•   Source: SciCrunch Registry

https://github.com/qiicr/dcmqi

Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer.

Proper citation: dcmqi (RRID:SCR_016933) Copy   

•   Source: SciCrunch Registry

https://www.wizardmac.com

Software tool for data analysis and exploration. Statistics software for Mac.

Proper citation: Wizard (RRID:SCR_016939) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/neurolucida360

Software for automatic neuron 3D reconstruction and analysis. Used by neuroscientists to reconstruct intricate neuronal structures that range in scale from complex, multicellular networks of neurons to sub-cellular dendritic spines and putative synapses.

Proper citation: Neurolucida 360 (RRID:SCR_016788) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/us/en/home/life-science/cell-analysis/cellular-imaging/high-content-screening/high-content-screening-instruments/hcs-studio-2.html

Software packages for quantitative cell analysis. Used in image cytometry, quantitative cell analysis or automated cell analysis in biological research and drug discovery.

Proper citation: HCS Studio Cell Analysis software (RRID:SCR_016787) Copy   

•   Source: SciCrunch Registry