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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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pyLMM Resource Report Resource Website 10+ mentions |
pyLMM (RRID:SCR_014525) | data analysis software, data processing software, software application, software resource, standalone software | A Python package for doing linear mixed model associations in genome wide association studies (GWAS). The software corrects for population structure using EMMA. | python, data analysis software, linear mixed model, genome wide association studies, gwas, lmm, emma | DOI:10.1534/genetics.107.080101 | Install using pip | SCR_014525 | 2026-09-12 12:58:18 | 12 | ||||||||||
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ENIGMA-DTI Pipeline Resource Report Resource Website 50+ mentions |
ENIGMA-DTI Pipeline (RRID:SCR_014649) | protocol | Pipeline which provides tools to extract whole-brain average and regional measurements from DTI images including FA, AD, RD and MD. Protocols for preprocessing, ENIGMA-DTI processing (skeletonization and ROI extraction), and GWAS analysis are available. Software tools used for each process are listed within the protocols. | dti, enigma, protocol, pipeline |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Southern California; Los Angeles; USA has parent organization: ENIGMA |
NIBIB U54 EB020403 | Available for download from NITRC | http://www.nitrc.org/projects/enigma_dti | SCR_014649 | ENIGMA-DTI protocol, ENIGMA DTI pipeline, ENIGMA DTI protocol | 2026-09-12 12:58:20 | 50 | |||||||
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VitalView Software Resource Report Resource Website 10+ mentions |
VitalView Software (RRID:SCR_014497) | data acquisition software, data analytics software, data processing software, software application, software resource | A data acquisition and analysis software program. The program collects data from sensors and receivers and displays graphical data analysis as well as descriptive statistics. | data acquisition, data analysis | PMID:12213503 | Commercial | SCR_014497 | 2026-09-12 12:58:17 | 16 | ||||||||||
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GUID Tool Resource Report Resource Website 1+ mentions |
GUID Tool (RRID:SCR_014530) | data access protocol, software resource, web service | A customized software application that generates a Global Unique Identifier for each study participant. The GUID is a universal subject ID that allows researchers to share data specific to a study participant without exposing personally identifiable information (PII). The GUID has been approved by the NIH Office of General Counsel. | web service, universal subject id | is hosted by: NIMH Data Archive | For use when collaborating and sharing information | SCR_014530 | 2026-09-12 12:58:18 | 3 | ||||||||||
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HIPPIE Resource Report Resource Website 100+ mentions |
HIPPIE (RRID:SCR_014651) | software resource, web application | Web tool used to generate confidence scored and functionally annotated human protein-protein interaction networks. Users can run a protein query using a UniProt identifier (ID or accession), gene symbol or Entrez gene id, or a network query using set fields. | web tool, web application, protein protein interaction, reference tool, protein query, network query, human protein protein interaction network | Helmholtz Alliance in Systems Biology ; BMBF 01GS08170 |
DOI:10.1371/journal.pone.0031826 | Available on the web, Available for download, Acknowledgement requested | SCR_014651 | Human Integrated Protein Protein Interaction Reference, Human Integrated Protein-Protein Interaction rEference, Human Integrated Protein-Protein Interaction rEference (HIPPIE) | 2026-09-12 12:58:20 | 142 | ||||||||
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LANDMark BioBanks Resource Report Resource Website 1+ mentions |
LANDMark BioBanks (RRID:SCR_014534) | biobank, biospecimen repository, data or information resource, data set, material storage repository, service resource, storage service resource | A repository of human tissue samples collected during the LANDMark study (Longitudinal Assessment of Neuropathy in Diabetes using novel ophthalmic markers). The LANDMark Biobank longitudinal dataset contains blood and tissue (skin) samples and matching detailed phenotypic data of three microvascluar complications of type 1 diabetes: neuropathy, nephropathy and retinopathy. | biospecimen repository, data set, type 1 diabetes, biobank, human tissue, landmark study, longitudinal data set, blood, skin, neuropathy, nephropathy, retinopathy | is listed by: NIDDK Information Network (dkNET) | Type 1 diabetes, Diabetes | Available to the research community, Apply to the Tissue Access Committee to access tissue samples | SCR_014534 | 2026-09-12 12:58:18 | 2 | |||||||||
|
RepeatScout Resource Report Resource Website 500+ mentions |
RepeatScout (RRID:SCR_014653) | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource | Algorithm used to identify de novo repeat families in newly sequenced genomes. Repeat libraries for C. briggsae, M. muscles (X chromosome), R. novegicus (X chromosome), armadillo, H. sapiens (X chromosome), and various other mammals created using RepeatScout are available on the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | algorithm, sequence analysis, repeat, genome sequence, de novo, repeat family, repeat library, bio.tools |
is used by: RepeatModeler is listed by: Debian is listed by: bio.tools has parent organization: University of California at San Diego; California; USA |
PMID:15961478 | THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:RepeatScout, biotools:RepeatScout | https://bio.tools/RepeatScout, https://bio.tools/RepeatScout, https://bio.tools/RepeatScout | SCR_014653 | 2026-09-12 12:58:20 | 818 | |||||||
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Mercator Resource Report Resource Website 500+ mentions |
Mercator (RRID:SCR_014493) | data analysis software, data processing software, software application, software resource | A software package for quantification of histological sections. This software performs functions including: management and analysis of regions of interest, annotations, statistical analysis, and 3D visualization. These results are edited in an Excel-compatible spreadsheet. | histology analysis, image analysis, statistical analysis, 3d visualization, excel | Commercial | SCR_014493 | 2026-09-12 12:58:17 | 692 | |||||||||||
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ImageMagick Resource Report Resource Website 100+ mentions |
ImageMagick (RRID:SCR_014491) | data processing software, image processing software, software application, software resource | Software suite for creating, editing, composing, and converting bitmap images. It can read and write images in over 200 formats including PNG, JPEG, JPEG-2000, GIF, TIFF, DPX, EXR, WebP, Postscript, PDF, and SVG. The user can use this software to resize, flip, mirror, rotate, distort, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves. | image editing, image processing software, image analysis software, bitmap, adjust image colors, bezier curves | is listed by: Debian | Restricted | https://sources.debian.org/src/imagemagick/ | SCR_014491 | 2026-09-12 12:58:17 | 140 | |||||||||
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pubatlas.org Resource Report Resource Website 1+ mentions |
pubatlas.org (RRID:SCR_014538) | data processing software, data visualization software, software application, software resource | A program that searches PubMed to generate a heat map using a user's search terms. It also allows you to see over the years how many publications there are with the user's search term(s). | atlas, pubmed, heat map, search term, data visualization | PMID:21347177 | SCR_014538 | PubAtlas: Association Explorer, PubAtlas | 2026-09-12 12:58:18 | 4 | ||||||||||
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NIRStar Resource Report Resource Website 50+ mentions |
NIRStar (RRID:SCR_014540) | data acquisition software, data processing software, software application, software resource | Commercial software tool designed to function as a multiplatform instrument controlling environment for NIRx products. Its features include the ability to run full or partial sensing configurations, montage views and viewing options, and a real-time system status reporting display. | multiplatform, instrument controlling environment, investigational, paradigm, imaging system, data acquisition software | has parent organization: NIRx NIRS Neuroimaging | Commercially available | SCR_014540 | NIRStar - NIRS Acquisition Software by NIRx, NIRStar, NIRS Acquisition Software by NIRx | 2026-09-12 12:58:18 | 57 | |||||||||
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Preclinical Data Forum Network Resource Report Resource Website 1+ mentions |
Preclinical Data Forum Network (RRID:SCR_014545) | data or information resource, discussion, forum, narrative resource | A forum for preclinical data sharing and interpretation to enhance its utility for clinical research and development. The forum allows researchers to communicate and collaborate on modern preclinical issues and data sharing. | forum, network, preclinical, research and development, data sharing | has parent organization: ECNP | DOI:10.1016/j.euroneuro.2015.05.011 | Available to the research community | SCR_014545 | Preclinical Data Forum Network of the ECNP, Preclinical Data Forum Network of the European College of Neuropsychopharmacology, European College of Neuropsychopharmacology - Preclinical Data Forum Network | 2026-09-12 12:58:18 | 1 | ||||||||
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Cell Line Authentication Testing Resource Report Resource Website 1+ mentions |
Cell Line Authentication Testing (RRID:SCR_014504) | CLA | quality control testing; authentication testing | A material analysis service of the commercial organization Genetica DNA Laboratories which provides authentication of human cancer cell lines, stem cell lines and xenografts utilizing STR DNA technology. | str profiling, cell line authentication, genetica, cancer cell line, stem cell line, xenograft | is related to: Genetica DNA Laboratories | PMID:20614197 | Available to the research community, Commercial | SCR_014504 | Genetica DNA Laboratories Cell Line Authentication, cell line identification testing; cell authentication | 2026-09-12 12:58:17 | 4 | |||||||
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International Geo Sample Number Resource Report Resource Website 1+ mentions |
International Geo Sample Number (RRID:SCR_014505) | IGSN | data or information resource, identifier resolution, international standard specification, narrative resource, production service resource, service resource, standard specification | A persistent unique identifier for samples and specimens collected from the natural environment. IGSNs are created by the user and are case sensitive. They should be concise, machine readable, and non-derivable to ensure originality. IGSNs were created and are organized by the IGSN e.V., whose goal is to implement and promote standard methods for locating, identifying, and citing physical samples with confidence by operating an international IGSN registration service with a distributed infrastructure for use by and benefit to its members. | identifier, natural environment, geology, unique, identifying system | Available to participating members, IGSNs must be tagged in manuscripts | http://igsn.github.io http://igsn.github.io/syntax | SCR_014505 | International GeoSample Number, International Geo Sample Number (IGSN) | 2026-09-12 12:58:17 | 2 | ||||||||
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I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | data analysis software, data processing software, software application, software resource | Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation. | Automated prediction, protein structure prediction, protein function prediction, protein 3D structure, amino acid sequence, alignment, simulation, 3D atomic model, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Kansas; Kansas; USA |
NIGMS GM083107; NIGMS GM084222 |
DOI:10.1186/1471-2105-9-40 DOI:10.1093/nar/gkv342 PMID:20360767 PMID:18215316 |
Free, Available for download, Freely available | biotools:i-tasser, SCR_018803 | https://bio.tools/i-tasser | SCR_014627 | Iterative Threading Assembly Refinement, Iterative Threading ASSEmbly Refinement | 2026-09-12 12:58:19 | 3874 | |||||
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GenStat Resource Report Resource Website 1000+ mentions |
GenStat (RRID:SCR_014595) | software resource | A statistical software which can be used for basic statistics, experimental design, sample size calculations, and analysis of linear mixed models, time series, and spatial analysis. | statistics, statistical, experimental design, linear mixed model, time series, spatial, size calculation, sample size | SCR_014595 | 2026-09-12 12:58:19 | 1747 | ||||||||||||
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7500 Real-Time PCR Software Resource Report Resource Website 10+ mentions |
7500 Real-Time PCR Software (RRID:SCR_014596) | data acquisition software, data processing software, software application, software resource | A software used to control and operate the Applied Biosystems 7500 Real-Time PCR system. | pcr, applied biosystem, control, operate, hardware management software, systems management software | Commercial, Paired with a PCR system | SCR_014596 | Applied Biosystems 7500 Real-Time PCR Software, 7500 Real Time PCR Software | 2026-09-12 12:58:19 | 43 | ||||||||||
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Thermo Xcalibur Resource Report Resource Website 5000+ mentions |
Thermo Xcalibur (RRID:SCR_014593) | data acquisition software, data processing software, software application, software resource | A software which acquires and processes data sets, primarily through the Xcalibur system. | data acquisition software, thermo fisher, xcalibur, excalibur, data set | SCR_014593 | 2026-09-12 12:58:19 | 8269 | ||||||||||||
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Cufflinks Resource Report Resource Website 5000+ mentions |
Cufflinks (RRID:SCR_014597) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality. | transcriptome, rna-seq, rna seq, cuffmerge, cufflink, cuffcompare, transfrags, artifacts, gtf file, transcriptome assembly, expression analysis, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite works with: GeneScissors is hosted by: GitHub |
DOI:10.1038/nbt.1621 | Acknowledgement requested, Source code available on GitHub | biotools:cufflinks, OMICS_01304, SCR_013307 | https://github.com/cole-trapnell-lab/cufflinks, https://bio.tools/cufflinks, https://sources.debian.org/src/cufflinks/ | SCR_014597 | 2026-09-12 12:58:19 | 9083 | |||||||
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SigmaGel Software Resource Report Resource Website 100+ mentions |
SigmaGel Software (RRID:SCR_014598) | data analysis software, data processing software, software application, software resource | Gel analysis software which can be used on a PC with TWAIN-compatible scanners without specialty equipment. Users scan or load an image which can then be calibrated. SigmaGel allows users to make lane measurements, spot measurements, and molecular weight measurements. After data analysis was completed, users can print or copy and paste data and images. | gel, gel analysis software, twain, data analysis | Available from SPSS Software | SCR_014598 | SigmaGel | 2026-09-12 12:58:19 | 151 |
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