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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Software tool as computational predictor of mammalian m(6)A site. Used for prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features.
Proper citation: SRAMP (RRID:SCR_024500) Copy
http://rna.tbi.univie.ac.at//cgi-bin/RNAWebSuite/RNAfold.cgi
Web server predict secondary structures of single stranded RNA or DNA sequences.
Proper citation: RNAfold (RRID:SCR_024427) Copy
https://nano-measurer.software.informer.com/
Software tool to process micrograph images for particle size.
Proper citation: Nano Measurer (RRID:SCR_024493) Copy
https://topospro.com/software/
Software package for analysis of geometrical and topological properties of periodic structures including crystals, networks, tilings.ToposPro was tailored to process large samples of crystallographic data and to find correlations between structure parameters.
Proper citation: ToposPro (RRID:SCR_024496) Copy
https://www.cs.cmu.edu/~jernst/stem/
Software tool for analysis of short time series gene expression data. Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments. Allows to identify significant temporal expression profiles and genes associated with these profiles and to compare behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology.
Proper citation: Stem (RRID:SCR_024499) Copy
Instrument control and data acquisition software for Agilent Seahorse XFe96 and XFe24 analyzers with Windows 10 64-bit OS only. Experiment design, instrument control, data analysis, and file management software. Software provides intuitive interface with predefined assay templates and streamlined experimental design for simplified metabolic analysis.
Proper citation: Agilent Seahorse Wave (RRID:SCR_024491) Copy
https://swissmodel.expasy.org/lddt
Web server for local superposition free score for comparing protein structures and models using distance difference tests. Superposition free score that evaluates local distance differences of all atoms in model, including validation of stereochemical plausibility.
Proper citation: lDDT (RRID:SCR_024524) Copy
https://github.com/adamallo/SimPhy
Software package for simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer, all three potentially leading to species tree/gene tree discordance and gene conversion. Used for phylogenomic simulation of gene, locus, and species trees.
Proper citation: SimPhy (RRID:SCR_024501) Copy
http://mutationassessor.org/r3/
Web server predicts functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. Functional impact is assessed based on evolutionary conservation of affected amino acid in protein homologs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Mutation Assessor (RRID:SCR_024502) Copy
https://github.com/pinellolab/CRISPResso2
Software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments.
Proper citation: CRISPResso2 (RRID:SCR_024503) Copy
https://silebat.github.io/FSK-Lab/openbugs.html
Software for analysing complex statistical models using Markov chain Monte Carlo methods.
Proper citation: OpenBUGS (RRID:SCR_024488) Copy
https://github.com/bzhanglab/AutoRT/
Software tool for peptide retention time prediction using deep learning. Supports peptide retention prediction for tryptic peptides, MHC bound peptides and PTM peptides.
Proper citation: AutoRT (RRID:SCR_024513) Copy
https://www.reading.ac.uk/bioinf/ModFOLD/
Web server for the global and local quality estimation of 3D protein models
Proper citation: ModFOLD (RRID:SCR_024518) Copy
A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data.
Proper citation: Metscape (RRID:SCR_014687) Copy
http://www.bic.mni.mcgill.ca/software/minc/
A medical imaging data format and an associated set of tools and libraries including a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction.
Proper citation: MINC (RRID:SCR_002391) Copy
Software which creates phylogenetic trees from molecular, morphological and/or behavioral data through high speed computer analysis.
Proper citation: PAUP (RRID:SCR_014931) Copy
https://www.vicon.com/products/software/nexus
Data capture software for use with Vicon motion capture system. Its features include MATLAB integration, Python pre-installed, customized workflow, and automated quality assessment.
Proper citation: Nexus (RRID:SCR_015001) Copy
http://www.statgraphics.com/download-statgraphics-centurion-xvii
Data analysis and visualization software with features that include a R interface, demographic maps, bivariate density estimation, multiple time series visualization, repeated ANOVA measures, and a multivariate visualizers.
Proper citation: Statgraphics Centurion (RRID:SCR_015248) Copy
Statistical modeling program that provides a wide choice of models, estimators, and algorithms in a program that has graphical displays of data and analysis results. Mplus allows the analysis of both cross-sectional and longitudinal data, single-level and multilevel data, data that come from different populations with either observed or unobserved heterogeneity, and data that contain missing values. Analyses can be carried out for observed variables that are continuous, censored, binary, ordered categorical (ordinal), unordered categorical (nominal), counts, or combinations of these variable types. In addition, Mplus has extensive capabilities for Monte Carlo simulation studies, where data can be generated and analyzed according to any of the models included in the program. The Mplus modeling framework draws on the unifying theme of latent variables. The generality of the Mplus modeling framework comes from the unique use of both continuous and categorical latent variables. Continuous latent variables are used to represent factors corresponding to unobserved constructs, random effects corresponding to individual differences in development, random effects corresponding to variation in coefficients across groups in hierarchical data, frailties corresponding to unobserved heterogeneity in survival time, liabilities corresponding to genetic susceptibility to disease, and latent response variable values corresponding to missing data. Categorical latent variables are used to represent latent classes corresponding to homogeneous groups of individuals, latent trajectory classes corresponding to types of development in unobserved populations, mixture components corresponding to finite mixtures of unobserved populations, and latent response variable categories corresponding to missing data.
Proper citation: MPlus (RRID:SCR_015578) Copy
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
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