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https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET
Software tool which deletes non-brain tissue from image of the whole head and estimates both internal and external skull surfaces.
Proper citation: Brain Extraction Tool (RRID:SCR_014586) Copy
http://www.qsrinternational.com/nvivo-product
Software suite for qualitative data analysis for text-based data and higher-order forms of data. Various packages are available and are dependent on the system used and the type of data analysis needed.
Proper citation: NVivo (RRID:SCR_014802) Copy
https://www.mathworks.com/products/simulink/
Block diagram environment that contains a graphical editor, customizable block libraries, and solvers for multidomain simulation and model-based design in MATLAB. It supports simulation, automatic code generation, and continuous test and verification of embedded systems.
Proper citation: Simulink (RRID:SCR_014744) Copy
http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm
Drug discovery software package which can be used in structure-based design, fragment-based design, pharmacophore discovery, medicinal chemistry, protein and antibody modelling, and molecular modeling and simulations. Each aspect of the software package has its own unique features: for example, features for structure-based design include active site detection, scaffold replacement, multi fragment search, and solvent analysis.
Proper citation: MOE (RRID:SCR_014882) Copy
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.
Proper citation: Bowtie 2 (RRID:SCR_016368) Copy
http://spider.science.strath.ac.uk/sipbs/software_ses.htm
Windows software program for recording and analyzing signals from whole cell voltage and current clamp experiments. Its features include automatic waveform measurement, quantal content analysis, command voltage pulse generation, and spontaneous event detection.
Proper citation: WinWCP (RRID:SCR_014713) 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
Software tool that can match tandem mass spectra with peptide sequences, in process known as protein identification. Database search engine for matching tandem mass spectra with protein sequences. Command line tool for matching tandem mass spectra with peptide sequences.
Proper citation: X!Tandem (RRID:SCR_015645) Copy
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
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
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
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
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
Platform for quantitative and qualitative proteomics research for Waters Corporation proteomics systems.
Proper citation: ProteinLynx Global Server (RRID:SCR_016664) Copy
https://www.schrodinger.com/maestro
Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data.
Proper citation: Maestro (RRID:SCR_016748) Copy
http://www.cb.uu.se/~amin/BlobFinder/
Software that can perform calculations on cells from fluorescence microscopy images. BlobFinder can perform two types of analysis: an average count analysis to count the number of fluorescent signals and nuclei in an image, and a single cell analysis to simulate a cytoplasm and assign each signal to a particular cell.
Proper citation: BlobFinder (RRID:SCR_015788) Copy
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