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http://www.kitware.com/opensource/volview.html
A software for volume visualization that can be used by researchers to explore and analyze medical and scientific data. This software uses a variety of tools to load and visualize the data on either a 2D or 3D display. Theses tools include volume rendering, maximum intensity projections and oblique reformatting. Visualizations can be saved mid-session and be reopened at a later time.
Proper citation: VolView (RRID:SCR_014569) Copy
http://factominer.free.fr/index.html
Software R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables.
Proper citation: FactoMineR (RRID:SCR_014602) Copy
Ratings or validation data are available for this resource
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
Proper citation: FastQC (RRID:SCR_014583) 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
https://aceabio.com/product/rtca-dp/
Data acquisition and analysis software used for xCELLigence Real Time Cell Analysis SP, DP and MP instruments. The software is used to program and execute experiments and analyze data.
Proper citation: RTCA Software (RRID:SCR_014821) Copy
http://www.biotech.uconn.edu/resources/biophysics
Software for analyzing sedimentation equilibrium (SE) data from analytical ultracentrifugation experiments. It uses a model-dependent simulation of data for matching data in order to determine when equilibrium has been achieved.
Proper citation: HeteroAnalysis (RRID:SCR_014991) 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
A Web-based Analysis Tool for Indirect Calorimetry Experiments which measure physiological energy balance. It is a web application for indirect calorimetry analysis which generates customizable time, bar and regression plots for calorimetry data using two-, three-, and four-group templates.
Proper citation: CalR (RRID:SCR_015849) Copy
https://github.com/jdiedrichsen/pcm_toolbox
Software for a Bayesian approach for evaluating representational models that specify how complex patterns of neural activity relate to visual stimuli, motor actions, or abstract thoughts. PCM evaluates the ability of models to predict novel brain activity patterns and integrates over all possible activity profiles and computes the marginal likelihood of the data under the activity profile distribution specified by the representational model.
Proper citation: Pattern Component Modelling Toolbox (RRID:SCR_015891) Copy
Developer of software tools for genomic research focused on computational methods of high throughput biomedical data analysis, including software to support next generation sequencing technologies, transcriptome analysis with RNASeq data, SNP detection and selection of disease specific SNP subsets. Provides custom genome annotation services.
Proper citation: SoftBerry (RRID:SCR_000902) Copy
APIs for Net Station data files. APIs are available for C++, C#, and Java.
Proper citation: Net Station API (RRID:SCR_000867) Copy
Software to simplify the processing of large rRNA sequence libraries (including single-strand and paired-end reads) obtained through high-throughput sequencing technology. Tools for assembly, quality filtering, taxonomy based analysis and taxonomy independent analysis tools, and tools to convert the data to formats suitable for common ecological and statistical packages are available. For extremely large datasets, command line tools are available.
Proper citation: RDPipeline (RRID:SCR_001192) Copy
http://www.bumc.bu.edu/cardiovascularproteomics/cpctools/strap/
Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible
Proper citation: STRAP (RRID:SCR_005675) Copy
Software tool to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types.
Proper citation: CellProfiler Image Analysis Software (RRID:SCR_007358) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. An integrated packages of tools for microarray data analysis. GEPAS provides a web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-color microarray experiments and other preprocessing options), to the final step of the functional profiling of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), which include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management.
Proper citation: Gene Expression Profile Analysis Suite (RRID:SCR_008341) Copy
https://compumedicsneuroscan.com/products/by-name/curry/
Processing software for multimodal neuroimaging centered on combining functional data such as EEG and MEG with imaging data from MRI and CT to optimize source reconstruction. They are now combining Curry's strength with the acquisition and signal processing features of the SCAN software for a comprehensive EEG acquisition, data analysis, source localization and source imaging package.
Proper citation: CURRY (RRID:SCR_009546) Copy
http://marsbar.sourceforge.net/
A toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery.
Proper citation: MarsBaR region of interest toolbox for SPM (RRID:SCR_009605) Copy
Data analysis software for neurophysiology with a multitude of features, including: * Import of native data files created by many popular data acquisition systems * All standard histogram and raster analyses * Shift predictors in crosscorrelograms and color markers in perievent rasters * Joint PSTH, burst analysis and many more analyses of timestamped data * Spectral analysis of spike and continuous data * 3D data view and animation * Fully customizable WYSIWYG graphics * Custom analysis and batch mode processing with internal scripting language * Direct data link to Matlab and Excel * Statistical tests via direct link to R-project
Proper citation: NeuroExplorer (RRID:SCR_001818) Copy
http://www.neuronland.net/NLMorphologyConverter/NLMorphologyConverter.html
NLMorphologyConverter is a simple command-line program for converting between the various neuron morphology data formats which are used to describe the three-dimensional physical branching structure of biological neurons. The aim is to provide coverage of all formats, old and new, in which data is available online, and/or which are supported by free and commercial software packages (e.g. software for neuron reconstruction, generation, simulation, visualization, and analysis of neuron morphology). Permission is granted for this software to be freely copied. Main Features Currently 21 different morphology file formats fully or partially supported. Automatic detection of input file format. Faithful reproduction of output file formatting. Many command line options for manipulating the imported data Intensively tested using over 10000 publicly available morphology data files. Sponsors. This software is supported by NeuronLand.
Proper citation: Neuronland: NLMorphologyConverter (RRID:SCR_001817) Copy
http://www.oeb.harvard.edu/faculty/hartl/old_site/lab/publications/GeneMerge.html
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Proper citation: GeneMerge (RRID:SCR_005744) Copy
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