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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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HTSJDK Resource Report Resource Website 1+ mentions |
HTSJDK (RRID:SCR_024036) | software application, software resource | Software implementation of unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data. | accessing common file formats, SAM, VCF, manipulating HTS data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/htsjdk/, https://github.com/samtools/htsjdk | SCR_024036 | htsjdk | 2026-08-09 09:08:21 | 4 | ||||||||
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InsPecT Resource Report Resource Website 1+ mentions |
InsPecT (RRID:SCR_024038) | software application, software resource | Software tool to addresses several algorithmic problems in order to identify modified proteins.Software MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed. | addresses algorithmic problems, identify modified proteins, post-translational modification identification, | is listed by: Debian | PMID:16013882 | Free, Available for download, Freely available, | OMICS_02397 | https://sources.debian.org/src/inspect/ | SCR_024038 | Inspect, inspect | 2026-08-09 09:08:44 | 1 | ||||||
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brms Resource Report Resource Website 1+ mentions |
brms (RRID:SCR_023862) | software toolkit, software resource | Software package implements Bayesian multilevel models in R using probabilistic programming language Stan. | Bayesian multilevel models, R, probabilistic programming language Stan, | is listed by: CRAN | DOI:10.18637/jss.v080.i01 | Free, Available for download, Freely available | SCR_023862 | 2026-08-09 09:08:48 | 7 | |||||||||
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Brainreg Resource Report Resource Website 1+ mentions |
Brainreg (RRID:SCR_023858) | software application, software resource | Software Python based tool that registers the template brain (e.g. from the Allen Reference Atlas) to the sample image.Automated 3D brain registration with support for multiple species and atlases. | Allen Mouse Brain Reference Atlas, Allen Human Brain Atlas, Allen Reference Atlas, template brain registration, sample image, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023858 | 2026-08-09 09:08:20 | 6 | ||||||||||
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DeepSlice Resource Report Resource Website 1+ mentions |
DeepSlice (RRID:SCR_023854) | software toolkit, software resource | Software Python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning. | Allen Mouse Brain Atlas, Common Coordinate Framework, Allen Brain Atlas, Waxholm rat atlas, aligns histology, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023854 | 2026-08-09 09:08:20 | 4 | ||||||||||
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Bibus Resource Report Resource Website |
Bibus (RRID:SCR_023974) | software application, software resource | Bibliographic and reference management software. Allows to search, edit, and sort bibliographic records. | Bibliographic and reference management, bibliographic records, search bibliographic records, edit bibliographic records, sort bibliographic records, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/bibus/ | SCR_023974 | bibus | 2026-08-09 09:08:51 | 0 | ||||||||
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Cell Type Analysis Toolbox Resource Report Resource Website |
Cell Type Analysis Toolbox (RRID:SCR_023852) | software toolkit, software resource | Software toolbox is cell counting and distribution mapping platform which can be used to analyze serial two-photon tomography (STPT) data. | Allen Mouse Brain Atlas, cell counting and distribution mapping, serial two-photon tomography data, STPT data, data analysis, | is related to: Allen Institute for Brain Science | PMID:28985566 | Free, Freely available | SCR_023852 | 2026-08-09 09:08:48 | 0 | |||||||||
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Kaptive Resource Report Resource Website 10+ mentions |
Kaptive (RRID:SCR_024046) | software application, software resource | Software tool to report information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies. | report information, surface polysaccharide loci, genome assemblies, | is listed by: Debian | PMID:28348840 | Free, Available for download, Freely available, | OMICS_27932 | https://sources.debian.org/src/kaptive/ | SCR_024046 | kaptive | 2026-08-09 09:08:53 | 18 | ||||||
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JabRef Resource Report Resource Website 1+ mentions |
JabRef (RRID:SCR_024047) | software application, software resource | Open source, software cross platform citation and reference management tool.Helps to collect and organize sources, find the paper, discover the latest research. | citation and reference, management tool, collect and organize sources, find the paper, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/jabref-plugin-oo/, https://github.com/JabRef/jabref | SCR_024047 | jabref, JabRef Bibliography Management | 2026-08-09 09:08:45 | 4 | ||||||||
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KBibTeX Resource Report Resource Website |
KBibTeX (RRID:SCR_024048) | software application, software resource | Software tool as bibliography editor for KDE. Used in conjunction with Kile. BibTeX editor for KDE. KBibTeX's primary file format is BibTeX as known from LaTeX, but other formats such as RIS, PDF, or RTF can be imported and exported. | bibliography editor for KDE, bibliography editor, BibTeX editor for KDE, | is listed by: Debian | Restricted | https://sources.debian.org/src/kbibtex/ | SCR_024048 | kbibtex | 2026-08-09 09:08:21 | 0 | ||||||||
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Microsoft PowerPoint Resource Report Resource Website 100+ mentions |
Microsoft PowerPoint (RRID:SCR_023631) | software application, software resource | Presentation software developed by Microsoft Corporation. Part of Microsoft Office suite. Used for creating slideshows and delivering presentations. | Microsoft Corporation, Microsoft Office, creating slideshows, delivering presentations, presentation software, | Restricted | SCR_023631 | 2026-08-09 09:08:17 | 115 | |||||||||||
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Reads2Map Resource Report Resource Website 1+ mentions |
Reads2Map (RRID:SCR_023593) | software toolkit, software resource | Software package as collection of WDL workflows to build linkage maps from sequencing reads. WDL workflows to build genetic maps from sequencing reads. | Genetic Map, Linkage analysis, Variant Calling, Dosage Calling | National Council for Scientific and Technological Development 313269/2021-1; USDA National Institute of Food and Agriculture (NIFA); 2020-51181-32156 Bill and Melinda Gates Foundation; OPP1213329 European Union’s Horizon 2020 |
DOI:10.1101/2022.11.24.517847 | Free, Available for download, Freely available | SCR_023593 | 2026-08-09 09:08:42 | 1 | |||||||||
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Zonation 5 Resource Report Resource Website 1+ mentions |
Zonation 5 (RRID:SCR_023745) | software application, software resource | Spatial prioritization software used to identify priority areas to support conservation planning, land use planning, ecological impact avoidance and other similar tasks. | Spatial prioritization, identify priority areas, support conservation planning, land use planning, ecological impact avoidance, | Free, Available for download, Freely available | https://github.com/zonationteam/Zonation5 | SCR_023745 | Zonation 5 v1.0 | 2026-08-09 09:08:45 | 1 | |||||||||
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DESDEO Resource Report Resource Website 1+ mentions |
DESDEO (RRID:SCR_023502) | software toolkit, software resource | Software Python framework for interactive multiobjective optimization methods. | interactive multiobjective optimization, optimization methods, | DOI:10.1109/ACCESS.2021.3123825 | Free, Available for download, Freely available | https://desdeo.it.jyu.fi/, https://desdeo.readthedocs.io/en/latest/ | SCR_023502 | Decision Support for computationally Demanding Optimization | 2026-08-09 09:08:37 | 1 | ||||||||
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clusterSim Resource Report Resource Website 10+ mentions |
clusterSim (RRID:SCR_023743) | software toolkit, software resource | Software R package used for searching for optimal clustering procedure for data set. | searching for optimal clustering procedure for data set, optimal clustering procedure, data set clustering procedure, | is listed by: CRAN | Free, Freely available | SCR_023743 | 2026-08-09 09:08:40 | 21 | ||||||||||
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Aeskulap Resource Report Resource Website |
Aeskulap (RRID:SCR_023960) | software application, software resource | Software application as medical image viewer.Able to load series of special images stored in DICOM format for review. Able to query and fetch DICOM images from archive nodes (also called PACS) over the network. Designed to run under Linux. | medical image viewer, Digital Imaging and Communications in Medicine, DICOM, DICOM viewer, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/aeskulap/ | SCR_023960 | Aeskulap - DICOM Viewer, aeskulap | 2026-08-09 09:08:43 | 0 | ||||||||
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Gigapixel AI Resource Report Resource Website 1+ mentions |
Gigapixel AI (RRID:SCR_023684) | software application, software resource | Software to increase image resolution. Gigapixel AI’s neural networks are continuously trained on sample images to increase resolution of different subjects like portraits, wildlife, landscapes, architecture and image types like DSLR, web/compressed, CG. | Topaz Labs, increase image resolution, image resolution, | Restricted | SCR_023684 | Gigapixel AI Image Enhancement Software | 2026-08-09 09:08:18 | 1 | ||||||||||
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Frictionless Data Resource Report Resource Website 1+ mentions |
Frictionless Data (RRID:SCR_023713) | software toolkit, software resource | Open source software package for building data infrastructure including data management, data integration, data flows, etc. Includes various data standards and provides software to work with data. | building data infrastructure, data management, data integration, data flows, data standards information, | Free, Available for download, Freely available | https://github.com/frictionlessdata | SCR_023713 | 2026-08-09 09:08:45 | 7 | ||||||||||
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ABI-expression-data-generator Resource Report Resource Website |
ABI-expression-data-generator (RRID:SCR_023834) | software application, software resource | Software to download expression data from Allen Mouse Brain data portal ABI. This script will query database, download available data, convert it from the raw/mhd format to NIfTI, and register it to standard space. Package-manager-friendly archive of gene expression maps registered in SMRI standard space from the Allen Mouse Brain Atlas. | Allen Mouse Brain Atlas, gene expression maps, expression data, standard space registration, SMRI standard space, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023834 | 2026-08-09 09:08:19 | 0 | ||||||||||
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Rprs Resource Report Resource Website 1+ mentions |
Rprs (RRID:SCR_023557) | Rprs | software toolkit, software resource | Software R package for computing Polygenic Risk Scores from dosages. | computing Polygenic Risk Scores from Polygenic Risk Scores, Polygenic Risk Scores, Polygenic Risk Scores | Free, Available for download, Freely available | SCR_023557 | Polygenic Risk Scores | 2026-08-09 09:08:17 | 1 |
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