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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CHROMSCAN Resource Report Resource Website 1+ mentions |
CHROMSCAN (RRID:SCR_013131) | CHROMSCAN | software resource, software application | A statistical based program for association mapping of disease genes. It utilises the Malecot model and the linkage disequilibrium (LD) map for the candidate region to analyse the genotypes derive from large sample of matched cases and controls. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154272 | SCR_013131 | 2026-08-12 10:50:43 | 2 | |||||||||
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BOREL Resource Report Resource Website 10+ mentions |
BOREL (RRID:SCR_013135) | software resource, software application | Software application for inference of genealogical relationships from genetic data, including sibship inference. | gene, genetic, genomic, c, unix, (dec-unix/..) |
is listed by: Genetic Analysis Software is related to: PANGAEA |
nlx_154197 | http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml | ftp://ftp.u.washington.edu/pub/user-supported/pangaea/PANGAEA/BOREL | SCR_013135 | 2026-08-12 10:50:44 | 10 | ||||||||
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Clinical Trial Management Application Resource Report Resource Website |
Clinical Trial Management Application (RRID:SCR_013531) | CTMA | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 11, 2012. The Clinical Trials Management Tools are Java-based suite (accessed via a secure intranet) for managing various aspects of a clinical trial, research protocols, outcomes initiatives, statistical research analysis, as well as CTEP/CDUS reporting. Developed in collaboration with the Clinical Research Services (CRS) Office at the UPCI, this research-based application provides an integrated tool for managing administrative (e.g. IRB submissions and approvals) and clinical (e.g. tumor measurements, registrations/ screenings) functions for the collection and analysis of data generated from a clinical trial. More information can be found here, http://www.upci.upmc.edu/spore/skin/coreD.cfm | clinical trial, clinical, research protocol, outcomes initiative, statistical research analysis, ctep reporting, cdus reporting, clinical study, bioinformatics, computer platform, windows |
is listed by: Biositemaps has parent organization: University of Pittsburgh; Pennsylvania; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33266 | SCR_013531 | Clinical Trial Management Application (CTMA) | 2026-08-12 10:50:48 | 0 | |||||||
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GASSOC Resource Report Resource Website 10+ mentions |
GASSOC (RRID:SCR_013136) | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application for statistical methods for disease and genetic marker associations using cases and their parents. These methods include an extension of the transmission/disequilibrium test (TDT) for multiple marker alleles, as well as additional general tests sensitive to associations that depend on dominant or recessive genetic mechanisms. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, sunos, solaris | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154077 | SCR_013136 | Genetic ASSOCiation analysis software for cases and parent | 2026-08-12 10:50:42 | 13 | ||||||||
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MAPPOP Resource Report Resource Website 1+ mentions |
MAPPOP (RRID:SCR_013490) | MAPPOP | software resource, software application | Software application that selects high resolution mapping subsamples and performs bin mapping (entry from Genetic Analysis Software) | gene, genetic, genomic, matlab, unix, ms-windows, macos, etc | nlx_154467 | SCR_013490 | 2026-08-12 10:50:48 | 5 | ||||||||||
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SNPMSTAT Resource Report Resource Website |
SNPMSTAT (RRID:SCR_013339) | SNPMSTAT | software resource, software application | A command-line program for the statistical analysis of SNP-disease association in case-control/cohort/cross-sectional studies with potentially missing genotype data. SNPMStat allows the user to estimate or test SNP effects and SNP-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty, study design and gene-environment dependence. For SNPs without missing data, the program performs the standard association analysis. For typed SNPs with missing data or untyped SNPs, the program performs the maximum-likelihood analysis. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154647 | SCR_013339 | SNP Missing data STATistics | 2026-08-12 10:50:44 | 0 | ||||||||
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AFQ: Automated Fiber Quatification Resource Report Resource Website 10+ mentions |
AFQ: Automated Fiber Quatification (RRID:SCR_014546) | AFQ | data analytics software, software resource, software application | A framework for generating Tract Profiles of tissue properties for major fiber tracts in healthy and diseased brains. Online documentation can be found at: https://github.com/yeatmanlab/AFQ/wiki. AFQ has been tested for MATLAB r2009b through MATLAB r2014b. It requires functions from the MATLAB stats toolbox, vistasoft and SPM. | DTI | PMID:23166771 | Available under GNU General Public License | https://github.com/yeatmanlab/AFQ | SCR_014546 | 2026-08-12 10:51:07 | 22 | ||||||||
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MECPM Resource Report Resource Website |
MECPM (RRID:SCR_013341) | MECPM | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154070 | SCR_013341 | Maximum Entropy Conditional Probability Moldeling | 2026-08-12 10:50:46 | 0 | ||||||||
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Dexy Resource Report Resource Website |
Dexy (RRID:SCR_013982) | software resource, software application | A multi-purpose project automation tool written in Python which helps create technical documents. Dexy is a free-form literate documentation tool for writing any kind of technical document incorporating code. It provides a consistent interface to tools and scripts and keeps track of what to run, in which order, and with what parameters. | software application, Python, technical document, documentation tool, live code |
is listed by: Connected Researchers is related to: Connected Researchers |
OpenGamma | Open source | SCR_013982 | dexy | 2026-08-12 10:50:55 | 0 | ||||||||
|
CDE Tool Resource Report Resource Website |
CDE Tool (RRID:SCR_013981) | systems interoperability software, software resource, software application | A software application which automatically packages up the code, data, and environment required to deploy and run Linux programs on other machines without any installation or configuration. Users can prepend any set of Linux commands with the "cde" binary, and CDE will run them and automatically package up all files accessed during execution. A package is a directory that can be compressed and delivered to any x86-Linux machine and contains all the files and environment variables required to run the original commands. After receiving the package, the user can run those same commands from within the package on any modern x86-Linux distro., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | software application, CDE, Linux, systems interoperability software |
is listed by: Connected Researchers is related to: Connected Researchers |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/pgbovine/CDE/ | SCR_013981 | CDEpack | 2026-08-12 10:50:53 | 0 | ||||||||
|
imDEV Resource Report Resource Website 1+ mentions |
imDEV (RRID:SCR_014674) | systems interoperability software, software resource, software application | A software application of RExcel that integrates R into Excel as an embedded additon for omics tasks and analysis. It can be used specifically for tasks concerning multivariate data visualization, exploration, and analysis. imDev has interactive modules for dimensional reduction, prediction, feature selection, analysis of correlation, and generation of networked structures, all of which provide an integrated environment for systems level analysis of multivariate data. | statistical analysis, statistical analysis package, r, r package, excel, data visualization, feature selection, omics, systems interoperability, software, metabolomics, bio.tools |
is listed by: Metabolomics Workbench is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/bts439 | Supports Microsoft Excel versions 2003-2010 | biotools:imdev | https://sourceforge.net/projects/imdev/, https://bio.tools/imdev | SCR_014674 | Interactive modules for Data Exploration and Visualization, Interactive modules for Data Exploration and Visualization (imDEV) | 2026-08-12 10:51:09 | 8 | ||||||
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Avisoft SASLabPro Resource Report Resource Website 50+ mentions |
Avisoft SASLabPro (RRID:SCR_014438) | data analytics software, software resource, software application | Sound analysis software used to process and analyze animal acoustic communications. Its features include digital filtering, real-time spectrogram display, and advanced metadata management. Avisoft SASLabPro is designed to accommodate large numbers of sound files and includes organizational features, including labeling options for single point data and time section labels. | saslabpro, avisoft, spectrogram, digital filtering, sound analysis, animal acoustics, animal communication | Open Source, Public | SCR_014438 | 2026-08-12 10:51:03 | 51 | |||||||||||
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MAOS Resource Report Resource Website 10+ mentions |
MAOS (RRID:SCR_013351) | software resource, software application | Software application that implements valid and efficient statistical methods for meta-analysis of genomewide association studies with overlapping subjects. The current release performs logistic regression analysis of individual level data under the additive mode of inheritance. Data from genome-wide association studies are often analyzed jointly for the purposes of combining information from multiple studies of the same disease or comparing results across different disorders. In many instances, the same subjects appear in multiple studies. Failure to account for overlapping subjects can greatly inflate type I error when combining results from multiple studies of the same disease and can drastically reduce power when comparing results across different disorders. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++ | is listed by: Genetic Analysis Software | nlx_154452 | SCR_013351 | Meta-Analysis with Overlapping Subjects | 2026-08-12 10:50:45 | 25 | |||||||||
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Canvas X Resource Report Resource Website 100+ mentions |
Canvas X (RRID:SCR_014288) | software resource, software application | Illustration and communication software for engineers and technical graphics professionals that combines the ability to make 3D images while also applying filters and duatone images. The software has minimum precision levels and object illustration and image editing tools to keep data accurate throughout the authoring process. Users can accelerate and streamline the technical illustration workflow from initial import and design to final presentation, facilitate collaboration, and improve the overall productivity. Tutorials and technical documents are available on the website. | authoring tool, illustration software, engineer, technical graphics professional, technical illustration workflow | Restricted | SCR_014312 | SCR_014288 | 2026-08-12 10:50:55 | 245 | ||||||||||
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LigandScout Resource Report Resource Website 100+ mentions |
LigandScout (RRID:SCR_014889) | software resource, software application | Software that takes a macromolecular structure containing a bound ligand and identifies the key features on the ligand which are interacting with points on a protein. Its features include: automatic interpretation of PDB ligands using geometry, dictionaries and rule; advanced handling of co-factors, ions, water molecules and covalently bound ligands; pharmacophore export to Catalyst(tm), MOE(tm) and PHASE(tm) for virtual screening; and the ability to treat co-factors and water molecules as part of the ligand or part of the macromolecule. | pharmacophore, macromolecular structure, bound ligand, pdb ligand, virtual screening, ligad based pharmacore design | is listed by: SoftCite | Available for purchase | https://www.chemistryworld.com/ligandscout/1012019.article | SCR_014889 | 2026-08-12 10:51:11 | 413 | |||||||||
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PhoxX Controller Resource Report Resource Website |
PhoxX Controller (RRID:SCR_016309) | software resource, software application | Software application for PhoxX® Diode Laser to support Omicron products. It is related to uManager open source microscopy software for control of microscopes. | Omicron Laserage, diode, laser, control, microscope | Free, Freely available, Available for download | https://micro-manager.org/wiki/Omicron, http://www.omicron-laser.de/english/downloads/downloads.html | SCR_016309 | 2026-08-12 10:51:29 | 0 | ||||||||||
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AxIS Resource Report Resource Website 10+ mentions |
AxIS (RRID:SCR_016308) | AxIS | software resource, software application | Software for multi electrode array recording for Axion Biosystems. Used in enhancing cardiac and neural analysis through data processing and signal monitoring. | Axion BioSystems, multi, electrode, array, recording, | Commercially available | SCR_018760 | SCR_016308 | Axion Integrated Studio | 2026-08-12 10:51:32 | 33 | ||||||||
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CHARMM Resource Report Resource Website 500+ mentions |
CHARMM (RRID:SCR_014892) | simulation software, software resource, software application | Software program that simulates molecular interactions. It has features that allow broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques, and a range of implicit solvent models. It also primarily targets biological systems including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. CHARMM can also be applied to inorganic materials with applications in materials design and has a comprehensive set of analysis and model builiding tools. | visualization, modeling, molecular simulation, materials design, model building tools, analysis, biological systems, peptides, proteins | is used by: CHARMM-GUI | SCR_014892 | 2026-08-12 10:51:11 | 970 | |||||||||||
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FINDTHECAT Resource Report Resource Website 1+ mentions |
FINDTHECAT (RRID:SCR_016036) | software resource, software application | Software that conducts a jspsych test for response time evaluation. Used in the ABCD Study. | psych, jspsych, psychology, response, time, evaluation, task, test, abcd, adolescent | NIDA U24 DA041123 | Free, Available for download | SCR_016036 | 2026-08-12 10:51:18 | 1 | ||||||||||
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paint.net Resource Report Resource Website 10+ mentions |
paint.net (RRID:SCR_017641) | software resource, software application | Software tool as image and photo editor for PCs that run Windows. Features user interface with support for layers, unlimited undo, special effects, and variety of useful and powerful tools. | Image, photo, editor | PMID:18941840 | Free, Available for download, Freely available | SCR_017641 | paint.net 4.2.8, Paint.NET | 2026-08-12 10:51:48 | 15 |
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