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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.agilent.com/en/product/cell-analysis/real-time-cell-metabolic-analysis/xf-software/seahorse-wave-controller-software-2-6-1-740904

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.rna-society.org/rnalocate/

Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation.

Proper citation: RNALocate (RRID:SCR_024418) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.scandb.org/newinterface/about.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SCAN (RRID:SCR_005185) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/mammals/haploreg/haploreg.php

HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using linkage disequilibrium (LD) information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.

Proper citation: HaploReg (RRID:SCR_006796) Copy   

•   Source: SciCrunch Registry

http://mummer.sourceforge.net/

Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.

Proper citation: MUMmer (RRID:SCR_018171) Copy   

•   Source: SciCrunch Registry

http://services.bio.ifi.lmu.de/ProSAS

This database provides a unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. ProSAS comprehensively annotates protein structures for several Ensembl genomes and alternative transcripts can be analyzed on the protein structure and protein function level using the intuitive user interface of the database. Users can search based on Ensembl gene or Ensembl transcript ids, Gene descriptions, Uniprot gene names, Genes matching patterns, Swissprot/Uniprot identifiers or Affymetrix probeset ids.

Proper citation: ProSAS (RRID:SCR_007876) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/eeglab/

Interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data. First developed on Matlab 5.3 under Linux, EEGLAB runs on Matlab v5 and higher under Linux, Unix, Windows, and Mac OS X (Matlab 7+ recommended). EEGLAB provides an interactive graphic user interface (GUI) allowing users to flexibly and interactively process their high-density EEG and other dynamic brain data using independent component analysis (ICA) and/or time/frequency analysis (TFA), as well as standard averaging methods. EEGLAB also incorporates extensive tutorial and help windows, plus a command history function that eases users'' transition from GUI-based data exploration to building and running batch or custom data analysis scripts. EEGLAB offers a wealth of methods for visualizing and modeling event-related brain dynamics, both at the level of individual EEGLAB ''datasets'' and/or across a collection of datasets brought together in an EEGLAB ''studyset.'' For experienced Matlab users, EEGLAB offers a structured programming environment for storing, accessing, measuring, manipulating and visualizing event-related EEG data. For creative research programmers and methods developers, EEGLAB offers an extensible, open-source platform through which they can share new methods with the world research community by publishing EEGLAB ''plug-in'' functions that appear automatically in the EEGLAB menu of users who download them. For example, novel EEGLAB plug-ins might be built and released to ''pick peaks'' in ERP or time/frequency results, or to perform specialized import/export, data visualization, or inverse source modeling of EEG, MEG, and/or ECOG data. EEGLAB Features * Graphic user interface * Multiformat data importing * High-density data scrolling * Defined EEG data structure * Open source plug-in facility * Interactive plotting functions * Semi-automated artifact removal * ICA & time/frequency transforms * Many advanced plug-in toolboxes * Event & channel location handling * Forward/inverse head/source modeling

Proper citation: EEGLAB (RRID:SCR_007292) Copy   

•   Source: SciCrunch Registry

http://www.gelifesciences.com/webapp/wcs/stores/servlet/catalog/en/GELifeSciences-us/products/AlternativeProductStructure_16016/29000605

Software for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ImageQuant (RRID:SCR_014246) Copy   

•   Source: SciCrunch Registry

https://pathcore.bsd.uchicago.edu/Downloads/HTRC_ImageScUG.pdf

Slide image modification software that allows the user to adjust the magnification, compare slides, pan and zoom, annotate specific areas, and perform image analysis of digital slides. Users can create macros and algorithms to automate analysis and create plots, respectively., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ImageScope (RRID:SCR_014311) Copy   

•   Source: SciCrunch Registry

http://www.usadellab.org/cms/index.php?page=trimmomatic

Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.

Proper citation: Trimmomatic (RRID:SCR_011848) Copy   

•   Source: SciCrunch Registry