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

Software Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or python scripts to process the data.

Proper citation: pyxnat (RRID:SCR_002574) Copy   

•   Source: SciCrunch Registry

http://nipy.org/nipy

A complete Python environment for the analysis of structural and functional neuroimaging data. It currently has a full system for general linear modeling of functional magnetic resonance imaging (fMRI).

Proper citation: NIPY (RRID:SCR_002489) Copy   

•   Source: SciCrunch Registry

http://www.neurobs.com/

Stimulus delivery and experiment control program. Stimuli include auditory, 2D and 3D visual, and multimodal and experimental data include fMRI, ERP, MEG, psychophysics, eye movements, single neuron recording, and reaction time measures.

Proper citation: Presentation (RRID:SCR_002521) Copy   

•   Source: SciCrunch Registry

http://odr.stowers.org/websimr/

THIS RESOURCE IS NO LONGER IN SERVICE, documented January 13, 2022. Open access repository of original, unprocessed data underlying work published by Stowers researchers to allow the scientific community to validate and extend the findings made by Stowers researchers. For papers first submitted for publication after November 1, 2011, the Stowers Institute requires its members to deposit original data files into the Stowers Original Data Repository or to repositories maintained by third parties at the time of publication. Access to the Stowers Original Data Repository is free, but you will be asked to register before you can download data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Stowers Original Data Repository (RRID:SCR_002640) Copy   

•   Source: SciCrunch Registry

http://www.uark.edu/

Public, co educational research university in Fayetteville, Arkansas.

Proper citation: University of Arkansas; Arkansas; USA (RRID:SCR_002515) Copy   

•   Source: SciCrunch Registry

http://www.paraview.org/

Open source, multi platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.

Proper citation: ParaView (RRID:SCR_002516) Copy   

•   Source: SciCrunch Registry

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

Software package representing Spatial Statistical Parametric Mapping that includes two tools presently: MAGEE and FADTTS. MAGEE represents the Multiscale Adaptive Generalized Estimating Equation. It was developed specifically for analyzing multivariate neuroimaging data in 3-dimensional volume (or on 2-dimensional surface) from longitudinal neuroimaging studies. FADTTS represents Functional Analysis of Diffusion Tensor Tract Statistics. The aim of this tool is to implement a functional analysis pipeline, for delineating the structure of the variability of multiple diffusion properties along major white matter fiber bundles and their association with a set of covariates of interest, in various diffusion tensor imaging studies.

Proper citation: Spatial Statistical Parametric Mapping (RRID:SCR_002592) Copy   

•   Source: SciCrunch Registry

http://theobjects.com/en/products/scientific/index.php

Software with advanced visualization techniques and state-of-the-art volume rendering provide unparalleled insight into the details and properties of neurological data acquired by CT, micro-CT, MRI, PET, SPECT, microscopy and other modalities. With data fusion tools, intramodality and multimodality registration of MR/CT or PET/CT is easily accomplished, while semi-automatic VOI delineation on fused datasets can improve analysis. Standard formats, such as DICOM, RAW, JPEG, NIFTI, Analyze are supported and 3D/4D sequences can be played. Other features include MPR, oblique, CPR, volume clipping, and surface visualization of cortex, skull, and scalp models. Also standard are easy-to-use tools for voxel-based delineation of features and the measurement of properties, including areas, volumes, counts, and intensity profiles. Present your findings by creating annotated animations or high-resolution images for posters. An SDK is also available to create plug-ins that provide new workflows or functionalities.

Proper citation: ORS Visual SI (RRID:SCR_002509) Copy   

•   Source: SciCrunch Registry

http://rubioseq.sourceforge.net/

Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments.

Proper citation: RUbioSeq (RRID:SCR_002508) Copy   

•   Source: SciCrunch Registry

http://www.openmicroscopy.org/site/products/omero

Client-server software for management, visualization, and analysis of biological microscopy images. OMERO handles images in a secure central repository where users can view, organize, analyze and share data from anywhere with internet access. Work with images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software.

Proper citation: OMERO (RRID:SCR_002629) Copy   

•   Source: SciCrunch Registry

http://sites.google.com/site/marcocongedo/software/nica

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Software program, executable under any Windows32 OS, performs Group BSS (Blind Source Separation) analysis comparing two groups of individuals and it performs NICA (Normative ICA) analysis where individuals are compared individually to a (normative) group. All analysis is performed in the frequency domain, that is, for all frequencies. The program also performs all these analysis for qEEG, that is, at the electrode level, without any BSS. The program does all computations, saves and displays results. The rationale and methods used in this program are explained in all details in the following paper: Congedo M, John ER, De Ridder D, Prichep L (2010) Group Independent Component Analysis of Resting-State EEG in Large Normative Samples International Journal of Psychophysiology 78, 89-99.

Proper citation: Normative Independent Component Analysis (RRID:SCR_002506) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/wateRmelon.html

Software package for Illumina 450 methylation array normalization and metrics including 15 flavors of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages.

Proper citation: wateRmelon (RRID:SCR_001296) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngsrich/

Software for target enrichment performance for next-generation sequencing.

Proper citation: NGSrich (RRID:SCR_001333) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.10/bioc/html/oneChannelGUI.html

Software library that provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. The package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code.

Proper citation: oneChannelGUI (RRID:SCR_001325) Copy   

•   Source: SciCrunch Registry

http://itb.biologie.hu-berlin.de/~futschik/software/R/cycle/index.html

Software package for the identification of periodically expressed genes using Fourier analysis and the statistical assessment of significance using different background models.

Proper citation: CYCLE (RRID:SCR_001328) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.12/bioc/html/LMGene.html

Software package for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays.

Proper citation: LMGene (RRID:SCR_001329) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/affylmGUI/

R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11.

Proper citation: affylmGUI (RRID:SCR_001320) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/arrayQuality.html

Software functions for performing print-run and array level quality assessment.

Proper citation: arrayQuality (RRID:SCR_001315) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.10/bioc/html/ArrayTools.html

Software package for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.

Proper citation: ArrayTools (RRID:SCR_001313) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/affyPLM.html

Software for fitting probe-level models and tools using these models. Probe-level models (PLM) based quality assessment tools.

Proper citation: affyPLM (RRID:SCR_001319) Copy   

•   Source: SciCrunch Registry