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Portal provides information about nationwide study of more than 50,000 individuals to determine factors that predict disease severity and long-term health impacts of COVID-19.
Proper citation: Collaborative Cohort of Cohorts for COVID-19 Research (RRID:SCR_026322) Copy
https://github.com/tomcatsmith19/ArucoDetection
Automated rodent behavioral scoring system, complete with 3D design files and code/software. System monitors behavioral engagement using open-source software. 3D design files and necessary software has been made available, as well as code that can be used for data analysis.
Proper citation: ArUco (RRID:SCR_026572) Copy
https://github.com/Washington-University/HCPpipelines
Software package as set of tools, primarily shell scripts, for processing multi-modal, high-quality MRI images for the Human Connectome Project. Minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space.
Proper citation: HCP Pipelines (RRID:SCR_026575) Copy
https://endomap.hms.harvard.edu/
Structural interactome viewer. Interactive database of endosomal protein-protein interactions identified by cross-linking mass spectrometry and modeled by AlphaFold multimer. Structural protein interactome of human early endosomes.
Proper citation: EndoMap (RRID:SCR_026690) Copy
https://github.com/Yonghao-Holden/TEProf3
Software pipeline to detect Transposable Elements transcripts. Used to identify TE-derived promoters and transcripts using transcriptomic data from multiple sources, including short-read RNA-seq data, long-read RNA-seq data and single cell RNA-seq data.
Proper citation: TEProf3 (RRID:SCR_027288) Copy
https://github.com/smorabit/hdWGCNA
Software R package for performing weighted gene co-expression network analysis in high dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics.
Proper citation: hdWGCNA (RRID:SCR_027496) Copy
United States based educational platform dedicated to changing research culture by providing comprehensive educational materials, promoting best practices, and fostering a community committed to improving research reliability. Helps researchers learn and implement scientific rigor, such as proper experimental design, avoiding bias, and statistical analysis. Offers modules that address common issues such as experimental design, causal inference, avoiding statistical fallacies, and writing transparently reproducible code.
Proper citation: C4R (RRID:SCR_028702) Copy
Open source software for automated and manual tracing of neurites from light microscopy stacks of images. NCTracer 2.0 is developed for the Windows 7, 64-bit operating system and requires a minimum of 4 GB of RAM. This version does not run on 32-bit computers, Mac or Linux OS.
Proper citation: Neural Circuit Tracer (RRID:SCR_000116) Copy
http://www.fz-juelich.de/ime/spm_anatomy_toolbox
A MATLAB toolbox which uses three dimensional probabilistic cytoarchitechtonic maps to correlate microscopic, anatomic and functional data of the cerebral cortex. Correlating the activation foci identified in functional imaging studies of the human brain with structural (e.g., cytoarchitectonic) information on the activated areas is a major methodological challenge for neuroscience research. We here present a new approach to make use of three-dimensional probabilistic cytoarchitectonic maps, as obtained from the analysis of human post-mortem brains, for correlating microscopical, anatomical and functional imaging data of the cerebral cortex. We introduce a new, MATLAB based toolbox for the SPM2 software package which enables the integration of probabilistic cytoarchitectonic maps and results of functional imaging studies. The toolbox includes the functionality for the construction of summary maps combining probability of several cortical areas by finding the most probable assignment of each voxel to one of these areas. Its main feature is to provide several measures defining the degree of correspondence between architectonic areas and functional foci. The software, together with the presently available probability maps, is available as open source software to the neuroimaging community. This new toolbox provides an easy-to-use tool for the integrated analysis of functional and anatomical data in a common reference space.
Proper citation: SPM Anatomy Toolbox (RRID:SCR_013273) Copy
http://sourceforge.net/projects/powermap/
Software tool specifically designed for neuroimaging data that implements theoretical power calculation algorithms based on non-central random field theory. It can also calculate power for statistical analyses with FDR (false discovery rate) corrections. This GUI (graphical user interface)-based tool enables neuroimaging researchers without advanced knowledge in imaging statistics to calculate power and sample size in the form of 3D images. This tool is currently under limited release for beta testing. At this time, only users that have been directed to this site by the PowerMap developers will receive support.
Proper citation: PowerMap (RRID:SCR_006721) Copy
Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P-value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user-defined threshold. From RNA-Seq data can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.
Proper citation: rMATS (RRID:SCR_023485) Copy
Repository of person centered measures that evaluates and monitors physical, mental, and social health in adults and children.
Proper citation: Patient-Reported Outcomes Measurement Information System (RRID:SCR_004718) Copy
https://github.com/sccn/labstreaminglayer
System for unified collection of measurement time series in research experiments that handles networking, time synchronization, near real time access as well as optionally centralized collection, viewing and disk recording of data. System for synchronizing streaming data for live analysis or recording.
Proper citation: Lab Streaming Layer (RRID:SCR_017631) Copy
http://www.nitrc.org/projects/mni2orfromxyz/
Input either normalized MNI coordinates from a 3D image, or input real world XYZ matrix coordinates, and this code will convert coordinates of one type to the other.
Proper citation: Convert MNI coordinates to or from XYZ (RRID:SCR_000406) Copy
http://www.nitrc.org/projects/jist/
A native Java-based imaging processing environment similar to the ITK/VTK paradigm. Initially developed as an extension to MIPAV (CIT, NIH, Bethesda, MD), the JIST processing infrastructure provides automated GUI generation for application plug-ins, graphical layout tools, and command line interfaces. This repository maintains the current multi-institutional JIST development tree and is recommended for public use and extension. JIST was originally developed at IACL and MedIC (Johns Hopkins University) and is now also supported by MASI (Vanderbilt University).
Proper citation: JIST: Java Image Science Toolkit (RRID:SCR_008887) Copy
http://www.nitrc.org/projects/frats/
Software for the analysis of multiple diffusion properties along fiber bundle as functions in an infinite dimensional space and their association with a set of covariates of interest, such as age, diagnostic status and gender, in real applications. The resulting analysis pipeline can be used for understanding normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles.
Proper citation: Functional Regression Analysis of DTI Tract Statistics (RRID:SCR_002293) Copy
http://llama.mshri.on.ca/funcassociate/
A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool
Proper citation: FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) Copy
https://github.com/Cai-Lab-at-University-of-Michigan/nTracer
Software tool as plug-in for ImageJ software. Used for tracing microscopic images.
Proper citation: nTracer (RRID:SCR_023032) Copy
Software tool as robust preprocessing pipeline for functional MRI.Used for preprocessing of diverse fMRI data.
Proper citation: fMRIPrep (RRID:SCR_016216) Copy
http://mus.well.ox.ac.uk/mouse/INBREDS/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34.
Proper citation: Wellcome-CTC Mouse Strain SNP Genotype Set (RRID:SCR_003216) Copy
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