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https://sites.google.com/site/tdtdecodingtoolbox/

Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data.

Proper citation: The Decoding Toolbox (RRID:SCR_017424) Copy   

•   Source: SciCrunch Registry

https://www.qtiplot.com/

Software tool for data analysis and scientific visualization by IONDEV SRL.

Proper citation: QtiPlot (RRID:SCR_017311) Copy   

•   Source: SciCrunch Registry

http://vbspt.sourceforge.net/

Software package for analysis of single particle diffusion trajectories, where diffusion constants switch randomly according to Markov process. Analytical tool to combine information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. Has ability to learn number of diffusive states directly from data, in addition to model parameters such as transition rates and diffusion constants.

Proper citation: vbSPT (RRID:SCR_017554) Copy   

•   Source: SciCrunch Registry

http://sydney.edu.au/medicine/bosch/facilities/molecular-biology/nucleic-acid/corbett-rotor-gene.php

Rotor-Gene real-time analysis software system for ROTOR GENE 6000 REAL-TIME PCR machine. Software has been refined to provide an intuitive, Wizard driven interface, enabling flexibility and automation. Build-in extensive analysis, graphing and statistical functions. Unlimited use software license for Windows XP, Pentium IV (2GHz) or higher PC.

Proper citation: Rotor-Gene 6000 series software (RRID:SCR_017552) Copy   

•   Source: SciCrunch Registry

https://www.adinstruments.com/products/labchart

LabChart data analysis software creates a platform for all of your recording devices to work together, allowing you to acquire biological signals from multiple sources simultaneously and apply advanced calculations and plots as your experiment unfolds. LabChart Reader is free version of software that allows to analyse with some limitations. LabChart Reader doesn’t allow saving of data - export image only. Has data pad for analysis.

Proper citation: LabChart Reader (RRID:SCR_017551) Copy   

•   Source: SciCrunch Registry

https://www.mesquiteproject.org/

Software tool as modular system for evolutionary analysis. Software for evolutionary biology, designed to organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Analyses available depend on modules installed. Comes with many packages already installed.

Proper citation: Mesquite (RRID:SCR_017994) Copy   

•   Source: SciCrunch Registry

http://wbiomed.curtin.edu.au/genepop/

Population genetic data analysis software package. Used to perform exact Hardy Weinberg Equilibrium test. Used for population differentiation and for genotypic disequilibrium among pairs of loci. Computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc. and performs analyses of isolation by distance from pairwise comparisons of individuals or population samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GENEPOP (RRID:SCR_009194) Copy   

•   Source: SciCrunch Registry

https://github.com/macs3-project/MACS

Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.

Proper citation: MACS (RRID:SCR_013291) Copy   

•   Source: SciCrunch Registry

https://github.com/KM-Lab/Electrographic-Seizure-Analyzer

Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting.

Proper citation: Electrographic Seizure Analyzer (RRID:SCR_016344) Copy   

•   Source: SciCrunch Registry

https://amp.pharm.mssm.edu/biojupies/

Software as an open source web server that automatically generates RNA-seq data analysis of jupyter notebooks. It allows creation and containment of documents that have live code, visualizations and narrative text.

Proper citation: BioJupies (RRID:SCR_016346) Copy   

•   Source: SciCrunch Registry

http://saclab.tamu.edu/essentiality/transit/

Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions.

Proper citation: TRANSIT (RRID:SCR_016492) 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

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

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

http://www.thomaskoenig.ch/index.php/software/ragu

Software tool for the analysis of EEG and MEG event-related scalp field data using global randomization statistics.

Proper citation: Ragu (RRID:SCR_016851) 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/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

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://www.wizardmac.com

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

Proper citation: Wizard (RRID:SCR_016939) Copy   

•   Source: SciCrunch Registry