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https://www.embl-hamburg.de/biosaxs/dammif.html

Software tool for rapidly determining the low-resolution three-dimensional shape of biological macromolecules in solution using Small-Angle X-ray Scattering (SAXS) data. Used for rapid ab-initio shape determination in small-angle scattering.

Proper citation: DAMMIF (RRID:SCR_028444) Copy   

•   Source: SciCrunch Registry

https://bioconductor.posit.co/packages/3.20/data/annotation/html/IlluminaHumanMethylationEPICv2anno.20a1.hg38.html

Software R annotation package for Illumina's EPIC v2.0 methylation arrays. The version 2 covers more than 935K CpG sites in the human genome hg38. It is an update of the original EPIC v1.0 array (i.e., the 850K methylation array).

Proper citation: IlluminaHumanMethylationEPICv2anno (RRID:SCR_028569) Copy   

•   Source: SciCrunch Registry

https://gatk.broadinstitute.org/hc/en-us/articles/360036350452-VariantFiltration

Software command-line tool designed for hard-filtering variant callsets (VCF files) by applying user-defined criteria to annotate, rather than remove, low-quality variants. It marks fails in the FILTER field (e.g., using JEXL expressions to filter by DP, QD, or FS), making it essential for filtering small datasets, non-model organisms, or whenever Variant Quality Score Recalibration (VQSR) is not feasible

Proper citation: GATK VariantFiltration (RRID:SCR_028441) Copy   

•   Source: SciCrunch Registry

https://genome.ucsc.edu/goldenpath/help/bigWig.html

Command-line utility provided by the UCSC Genome Browser to convert text-based bedGraph files into indexed binary bigWig files. It is specifically used in bioinformatics to transform dense, continuous genome coverage data into a format that enables fast visualization and remote viewing in genome browsers like IGV or the UCSC Genome Browser.

Proper citation: bedGraphToBigWig (RRID:SCR_028439) Copy   

•   Source: SciCrunch Registry

https://www.scienceverse.org/metacheck/

Software R package to audit research outputs for compliance with open science best practices. Evaluates adherence to standards such as pre-registration and data availability. Used for automated checks of research outputs for best practices.

Proper citation: MetaCheck (RRID:SCR_028666) Copy   

•   Source: SciCrunch Registry

https://mycompounddiscoverer.com/

Software platform by Thermo Fisher Scientific designed for identifying, comparing, and interpreting small molecules in complex biological, environmental, and forensic samples. It uses customizable workflow, known as nodes, to automate mass spectrometry data processing, spectral library searching, and statistical analysis.Compound Discoverer is integrated with SIRIUS (via a custom workflow node) to bridge the gap between high-resolution MS/MS data and confident molecular identification. While Thermo Scientific’s Compound Discoverer excels at library searching and statistical analysis, SIRIUS provides powerful in silico tools to accurately predict molecular formulas, chemical classes, and de novo structures. High-resolution mass spectrometry (HRMS) data analysis software for untargeted metabolomics, lipidomics, and contaminant screening. Utilizes modular workflows to extract features, match spectra against libraries like mzCloud, and confidently identify complex organic compounds.

Proper citation: Compound Discoverer (RRID:SCR_028693) Copy   

•   Source: SciCrunch Registry

https://stoeltingco.com/Neuroscience/ANY-maze-Video-Tracking-Software~9825?navigate_from_document=1135&navigated_from_object=3955

Automated platform used in behavioral neuroscience to track and analyze the movements and behaviors of lab animals, such as mice and rats. Standardizes experiments like the Elevated Plus Maze, Open Field, Barnes Maze, and Fear Conditioning. Tracks whole-body movement, distance traveled, freezing/immobility, and zone entries. Connects to external devices like food dispensers, shockers, and lasers to trigger automated responses based on the animal's actions.

Proper citation: Stoelting ANY-maze Video Tracking Software (RRID:SCR_028718) Copy   

•   Source: SciCrunch Registry

https://insitupy.readthedocs.io/en/latest/

Software Python package for analysis of single-cell spatial transcriptomics data. Used to read, visualize, and analyze the spatially resolved gene expression within one dataset but also across different datasets. Provides general structure for organizing multiple datasets and its corresponding metadata.

Proper citation: InSitupy (RRID:SCR_028769) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/package=ppcor

Software R Package to calculates partial and semi-partial (part) correlations along with p-value. Fast Calculation to Semi-partial Correlation Coefficients.

Proper citation: ppcor (RRID:SCR_028755) Copy   

•   Source: SciCrunch Registry

https://github.com/dmcable/spacexr

Software R package for learning cell types and cell type-specific differential expression in spatial transcriptomics data. Used for cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics.

Proper citation: spacexr (RRID:SCR_028764) Copy   

•   Source: SciCrunch Registry

http://www.ccdc.cam.ac.uk/Solutions/CSDSystem

It records bibliographic, chemical and crystallographic information for organic molecules and metal-organic compounds whose 3D structures have been determined using X-ray diffraction and neutron diffraction.
The CSD records results of single crystal studies and powder diffraction studies which yield 3D atomic coordinate data for at least all non-H atoms. In some cases the CCDC is unable to obtain coordinates, and incomplete entries are archived to the CSD.
The CSD includes crystal structure data arising from:
* publications in the open literature
* Private Communications to the CSD (via direct data deposition)
The Cambridge Structural Database System (CSDS) is a single product that comprises the following components: The Cambridge Structural Database (CSD); CSDS Software: search and information retrieval (ConQuest), structure visualization (Mercury), statistical analysis of retrieved data (VISTA), and software for database creation (PreQuest); Knowledge bases derived from the CSD: Mogul (intramolecular geometry) and IsoStar (intermolecular interactions, including data from the PDB).
Cambridge Structural Database (CSD) is the world repository of small-molecule crystal structures. For example, the crystal structures supported by the National Institute on Drug Abuse are deposited here.

Proper citation: Cambridge Structural Data Base (RRID:SCR_007310) Copy   

•   Source: SciCrunch Registry

http://www.thebiogrid.org/

Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts.

Proper citation: Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) Copy   

•   Source: SciCrunch Registry

https://www.mc.vanderbilt.edu/victr/dcc/projects/acc/index.php/Main_Page

A national consortium formed to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research. The consortium is composed of seven member sites exploring the ability and feasibility of using EMR systems to investigate gene-disease relationships. Themes of bioinformatics, genomic medicine, privacy and community engagement are of particular relevance to eMERGE. The consortium uses data from the EMR clinical systems that represent actual health care events and focuses on ethical issues such as privacy, confidentiality, and interactions with the broader community.

Proper citation: eMERGE Network: electronic Medical Records and Genomics (RRID:SCR_007428) Copy   

•   Source: SciCrunch Registry

http://library.med.utah.edu/kw/brain_atlas/

Brain atlas in sagittal, coronal, and axial planes some from myelin stained sections, others from MRI. The structures are outlined and labeled on the zoomable images in the coronal series. The labels can also be used in quiz mode. Designed as part of of program for second year medical students studying neuroanatomy.

Proper citation: Atlases of the Brain (RRID:SCR_007293) Copy   

•   Source: SciCrunch Registry

https://ida.loni.usc.edu/login.jsp

Archive used for archiving, searching, sharing, tracking and disseminating neuroimaging and related clinical data. IDA is utilized for dozens of neuroimaging research projects across North America and Europe and accommodates MRI, PET, MRA, DTI and other imaging modalities.

Proper citation: LONI Image and Data Archive (RRID:SCR_007283) Copy   

•   Source: SciCrunch Registry

http://mipgsun.mipg.upenn.edu/~Vnews/

Data-, machine-, and application- independent software system for the visualization and analysis of multidimensional images. This transportable, very inexpensive software system, has capabilities for visualizing, manipulating, and analyzing multidimensional, multimodality image information. It is designed to run on Unix machines under X-windows. It uses a data protocol that is a multidimensional generalization of the ACR-NEMA standards. We have tested it extensively on SGI and Sun workstations and PCs. Other recipients of 3DVIEWNIX have installed it on a variety of platforms including IBM RS6000s, HP700s, and Stardent, all from a single source code version. UNIQUE FEATURES OF 3DVIEWNIX * Transportable - based on UNIX, X-window, and C * Based on multidimensional generalization of ACR-NEMA standards of data representation * Application-independent * Image dimensionality independent * Can handle rigid, non-rigid, static, and dynamic objects and object assemblies * Can handle object information from multiple modalities and longitudinal acquisitions * Multitudes of visualization, manipulation, and analysis methods incorporated * Open software system distributed with source code

Proper citation: 3DViewnix (RRID:SCR_007351) Copy   

•   Source: SciCrunch Registry

http://www.visionnetwork.nei.nih.gov/

The National Eye Institute (NEI) created the VISION Public Information Network for the purpose of communicating with public information officers at NEI grantee institutions. The Network''s primary mission is to work with the NEI in disseminating research results to the national and local media. The Network also works to inform the public of the mission of the National Institutes of Health (NIH) to improve the health of America through medical research. The NEI is part of the NIH, U.S. Department of Health and Human Services (DHHS). General information portal for eye and vision related resources for the public. Sponsors: This resource is supported by the National Eye Institute.

Proper citation: Vision Public Information Network (RRID:SCR_007340) Copy   

•   Source: SciCrunch Registry

http://ncmir.ucsd.edu/downloads/xvoxtrace.shtm

Xvoxtrace enables volume segmentation of tomographic data using manual tracing. This program allows the researcher to outline features on individual planes of the volume while being guided by simultaneous views of the tracing displayed on a volume rendering or tilt-series. Traced contours can be viewed using XDend or used to generate surfaces for viewing in Synu. Basic Requirements:OpenGL, X windows, and Linux platforms : :

Proper citation: Xvoxtrace (RRID:SCR_007377) Copy   

•   Source: SciCrunch Registry

http://www.i-mouse.org/

Over recent years, the European Commission has supported an increasing number of functional genomics projects focusing on the use of the laboratory mouse as a model of human disease. (see http://www.prime-eu.org/euromouseiiprojects.htm for a fuller listing of current and recent projects). CASIMIR (Coordination and Sustainability of International Mouse Informatics Resources: http://www.casimir.org.uk) is aimed at recommending standards to allow data sharing and integration between the different projects. CASIMIR spans a number of areas: data representation (in particular the use of shared ontologies), non-semantic, technical issues concerning database compatibility and interoperability, data acquisition, curation and ownership, integration of biological collections and material resources into the data network, and user interactions. As part of the CASIMIR initiative i-mouse.org was created as a common portal to CASIMIR and other resources we hope will be helpful for investigators using the mouse as a model system for humans or systems biologists and geneticists using the mouse as an experimental system. ontology; metadata;

Proper citation: Informatics resources for mouse functional genomics (RRID:SCR_007374) Copy   

•   Source: SciCrunch Registry

http://dblab.duhs.duke.edu/modules/dblabs_topcat/index.php

TOPPCAT stands for T-One weighted Perfusion imaging Parameter CAlculation Toolkit. TOPPCAT creates quantitative maps of Ktrans (volume transfer constant between blood plasma and the extravascular extracellular space) and fPV (fractional plasma volume) from dynamic T1-weighted perfusion images. At the current time, analysis using the method of Patlak plots (most appropriate for first pass dynamic contrast-enhanced MR imaging) is supported. As a preliminary step for the parameter calculation, TOPPCAT also creates maps of T1 and S0 (equilibrium magnetization) from multi-flip angle T1-weighted SPGR (or FLASH) sequences.Daniel P. Barboriak, James R. MacFall, Anthony O. Padua,Gerald E. York, Benjamin L. Viglianti, and Mark W. Dewhirst. Standardized software for calculation of Ktrans and vp from dynamic T1-weighted MR images. Presented at the International Society for Magnetic Resonance in Medicine Workshop on MR in Drug Development: From Discovery to Clinical Therapeutic Trials, McLean VA, April 2004.

Proper citation: T-One weighted Perfusion imaging Parameter CAlculation Toolkit (RRID:SCR_007376) Copy   

•   Source: SciCrunch Registry