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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Anatomography Resource Report Resource Website 1+ mentions |
Anatomography (RRID:SCR_018147) | web application, service resource, software resource | Web application that enables users to build and publish own custom manikins. Used to build three dimensional model of human body using parts registered in BodyParts3D. Server returns image of assembled 3D model as still image, rotating animation, interactive image, etc. Each part can be downloaded as polygon mesh file that can be used with 3D printer. | Custom manikins, 3D, body parts, three dimensional model, human body, image, rotating animation, interactive image, BodyParts3D, 3D printer | Free, Freely available | SCR_018147 | BodyParts3D / Anatomography | 2026-08-13 09:29:58 | 6 | ||||||||||
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smashpp Resource Report Resource Website 1+ mentions |
smashpp (RRID:SCR_018307) | data analysis software, data processing software, software application, data visualization software, software resource | Software tool to find and visualize rearrangements in DNA sequences. | Find sequence rearrangement, visualize sequence rearrangement, DNA, DNA sequence, DNA sequence rearrangement, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:smashpp, BioTools:smashpp | https://bio.tools/smashpp, https://bio.tools/smashpp, https://bio.tools/smashpp | SCR_018307 | Smash++ | 2026-08-13 09:30:11 | 2 | |||||||
|
ChromHMM Resource Report Resource Website 50+ mentions |
ChromHMM (RRID:SCR_018141) | data analysis software, data processing software, software resource, software application | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
NHGRI U54 HG004570; NHGRI RC1HG005334; NIEHS R01 ES024995; NHGRI U01 HG007912; NIMH U01 MH105578; NSF 0905968; Alfred P. Sloan Fellowship ; CAREER Award |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | 2026-08-13 09:30:17 | 50 | ||||||
|
GPS-SUMO Resource Report Resource Website 1+ mentions |
GPS-SUMO (RRID:SCR_018261) | data or information resource, data access protocol, service resource, web service, software resource, portal | Web service for prediction of SUMOylation sites and SUMO-interaction motifs in proteins by CUCKOO Workgroup. | Small ubiquitin like modifier, SUMOs, sumoylation, covalently modified protein, group prediction system, site prediction, interaction motif in protein, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; National Basic Research Program ; Guangdong Natural Science Funds for Distinguished Young Scholar ; Zhujiang Nova Program of Guangzhou ; International Science and Technology Cooperation Program of China |
PMID:24880689 | Restricted | biotools:gps-sumo | http://sumosp.biocuckoo.org/online.php, https://bio.tools/gps-sumo | SCR_018261 | Group-based Prediction System -Small Ubiquitin-like MOdifiers, Small Ubiquitin-like MOdifiers sp, GPS-SUMO 2.0, SUMOsp, GPS Small Ubiquitin-like MOdifiers, Group-based Prediction System-SUMO | 2026-08-13 09:30:11 | 6 | |||||
|
gProfiler2 Resource Report Resource Website 50+ mentions |
gProfiler2 (RRID:SCR_018190) | data analysis software, data processing software, software resource, software application | Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool. | Gene list, functional enrichment analysis, namespace conversion, data, analysis |
is listed by: ELIXIR Tools and Data Services Registry is related to: R Project for Statistical Computing works with: g:Profiler |
Estonian Research Council grants ; European Regional Development Fund for CoE of Estonian ICT research EXCITE projects |
PMID:31066453 | Free, Available for download, Freely available | SCR_018190 | gprofiler2 | 2026-08-13 09:30:18 | 63 | |||||||
|
Agisoft Metashape Resource Report Resource Website 100+ mentions |
Agisoft Metashape (RRID:SCR_018119) | data processing software, software application, standalone software, software resource, image processing software | Stand alone software that performs photogrammetric processing of digital images and generates 3D spatial data to be used in GIS applications, cultural heritage documentation, and visual effects production as well as for indirect measurements of objects of various scales. Successor of PhotoScan and is advanced image-based 3D modeling solution aimed at creating professional quality 3D content from still images. | Agisoft LLC, photogrammetry processing, digital image, 3D spatial data, GIS, visual effect production, 3D computer graphic |
is related to: Agisoft Photoscan is related to: Agisoft Photoscan |
SCR_018119 | 2026-08-13 09:30:09 | 172 | |||||||||||
|
RaptorX Resource Report Resource Website 100+ mentions |
RaptorX (RRID:SCR_018118) | data access protocol, simulation software, software application, web service, software resource | Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model. | Protein structure predictor, 3D structure, protein sequence, secondary and tertiary structure, binding site, solvent accessibility, disordered region, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Chicago; Illinois; USA |
NIGMS R01 GM089753; NSF DBI 0960390 |
PMID:21987485 | Restricted | biotools:raptorx | https://bio.tools/raptorx | SCR_018118 | 2026-08-13 09:30:16 | 198 | ||||||
|
FlowPy Resource Report Resource Website 1+ mentions |
FlowPy (RRID:SCR_018195) | data analysis software, data processing software, software application, data visualization software, software resource | Software Python tool for flow cytometry data. Data generated by flow cytometer can be read by FlowPy. Used for data extraction, data visualization, data clustering, histogram subtraction. | Flow cytometry data, data extraction, data visualization, data clustering, histogram subtraction | Free, Available for download, Freely available | SCR_018195 | 2026-08-13 09:30:18 | 2 | |||||||||||
|
VitalRecorder2 Resource Report Resource Website 1+ mentions |
VitalRecorder2 (RRID:SCR_018199) | data acquisition software, data processing software, software resource, software application | Sleep recording software by Kissei Comtech Co., Ltd. Can measure signals of up to 32 channels while monitoring wave forms in real time. Addition of video recording option enables simultaneous recording of biological signals and video. | Sleep recording, Kissei Comtech Co., Ltd., wave signal measure, wave form monitoring, biological signals recording | Restricted | SCR_018199 | 2026-08-13 09:30:18 | 4 | |||||||||||
|
SMART-Farm Tool Resource Report Resource Website 1+ mentions |
SMART-Farm Tool (RRID:SCR_018197) | SMART, SMART-Farm | web application, data or information resource, analysis service resource, production service resource, database, service resource, training service resource, software resource | Web and offline tool for holistic sustainability assessment of farms. Tool operationalizes Sustainability Assessment of Food and Agriculture Systems Guidelines of Food and Agriculture Organisation of United Nations. Tool consists of questionnaire software, centralized database, pool of indicators and scientifically based assessment methodology. Different stakeholders can use results of this assessment e.g. for comparing different farms, production systems or for strategic development, improvement, monitoring and communication to business partners. | Sustainability assessment, food company, organic agriculture, strategic development, monitoring, Sustainable Food Systems GmbH | https://www.sustainable-food-systems.com/smart-methode/, https://www.fibl.org/en/themes/projectdatabase.html | SCR_018197 | Sustainability Monitoring and Assessment RouTine, smart, SMART tool, smart farm, SMART-Farm tool | 2026-08-13 09:29:59 | 1 | |||||||||
|
UltraScan Resource Report Resource Website 10+ mentions |
UltraScan (RRID:SCR_018126) | data analysis software, data processing software, software resource, software application | Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis. | Hydrodynamic data, analytical ultracentrifugation experiment, data editing, analysis, sedimentation velocity experiment, spectrum analysis, genetic algorithm, Monte Carlo analysis | NSF DBI 9724273; NSF DBI 9974819; NSF ANI 228927; NSF TG-MCB 060019T; NSF TG-MCB 070038; NSF TG-MCB 070039; NSF TG-MCB 070040; NSF OCI 1032742; NSF ACI 1339649; NCRR RR022200; NCRR RR 022200 03S1; NIGMS GM120600; San Antonio Life Science Institute ; Howard Hughes Medical Institute ; Robert J. Kleberg Jr. and Helen C. Kleberg Foundation |
Free, Available for download, Freely available | SCR_018126 | 2026-08-13 09:30:17 | 20 | ||||||||||
|
HAST Resource Report Resource Website 1+ mentions |
HAST (RRID:SCR_018247) | data analysis software, data processing software, software resource, software application | Software tool for partition stLFR reads based on trio binning using prenatally unique markers. Haplotype resolved assembly for synthetic long reads using Trio-Binning strategy. | Partition stLFR reads, stLFR read, trio binning, haplotype resolved assembly, synthetic long read, reads assembly | Free, Available for download, Freely available | SCR_018247 | Haplotype-resolved Assembly for Synthetic long reads using a Trio-binning strategy | 2026-08-13 09:30:11 | 1 | ||||||||||
|
CLIP-Explorer Resource Report Resource Website 1+ mentions |
CLIP-Explorer (RRID:SCR_018128) | data analysis software, data processing software, software application, data visualization software, service resource, software resource | Webserver to process, analyse and visualise CLIP-Seq data. Software tools to process and visualise RNA protein interactions. CLIP-Seq data analysis in Galaxy. Galaxy CLIP-Explorer can process large CLIP-Seq data of eCLIP, iCLIP, and with simple changes to iCLIP workflows also FLASH, and uvCLAP. | CLIP-seq data, RNA protein interaction, Galaxy, data analysis, eCLIP, iCLIP, FLASH, uvCLAP, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: FLASH |
Restricted | SCR_018130, biotools:CLIP-Explorer | https://bio.tools/CLIP-Explorer | SCR_018128 | 2026-08-13 09:30:10 | 2 | ||||||||
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genomics resource for animal lectins Resource Report Resource Website 1+ mentions |
genomics resource for animal lectins (RRID:SCR_018122) | topical portal, data or information resource, portal | Resource presents information about animal lectins involved in various sugar recognition processes. | Genomic, animal lectin, sugar recognition process | has parent organization: Imperial College London; London; United Kingdom | BBSRC ; Wellcome Trust ; Consortium for Functional Glycomics |
Free, Freely available | SCR_018122 | 2026-08-13 09:30:16 | 3 | |||||||||
|
Stan Resource Report Resource Website 100+ mentions |
Stan (RRID:SCR_018459) | simulation software, software resource, programming language, software application | Probabilistic programming language for specifying statistical models. Defines log probability function over parameters conditioned on specified data and constants. Platform for statistical modeling and high performance statistical computation. Provides full Bayesian inference for posterior expectations including parameter estimation and posterior predictive inference by defining appropriate derived quantities of interest. | Statistical model specification, statistical modeling, statistical computation, log probability function, parameter, data, constant, parameter estimation | DOI:1509.07164 DOI:10.18637/jss.v076.i01 |
Free, Available for download, Freely available | SCR_018459 | 2026-08-13 09:30:04 | 221 | ||||||||||
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LUNGevity Resource Report Resource Website 1+ mentions |
LUNGevity (RRID:SCR_018570) | data or information resource, organization portal, funding resource, portal | Portal dedicated to funding lung cancer research by LUNGevity Foundation. Supports patient focused research and convene multi stakeholder meetings to streamline research process and accelerate progress to patients. Seeks to empower patients to be active decision makers in their treatment process through educational resources, online peer-to-peer support, and in-person survivorship programs. | Funding lung cancer, funding, lung cancer, LUNGevity Foundation, patient focused research support | lung cancer | Restricted | SCR_018570 | 2026-08-13 09:30:26 | 3 | ||||||||||
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Intensity Ratio Nuclei Cytoplasm Tool Resource Report Resource Website 10+ mentions |
Intensity Ratio Nuclei Cytoplasm Tool (RRID:SCR_018573) | data processing software, software application, image analysis software, software resource, image processing software | Software tool to calculate ratio of intensity in nuclei and cytoplasm. It needs two images as input cytoplasm channel and nuclei channel. | Intensity ratio, nuclei, cytoplasm, image, cytoplasm channel, nuclei channel, calculate ration, ImageJ | works with: ImageJ | Free, Freely available | SCR_018573 | 2026-08-13 09:30:06 | 37 | ||||||||||
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BioVelocity Resource Report Resource Website 1+ mentions |
BioVelocity (RRID:SCR_018501) | data analysis software, data processing software, software application, image analysis software, alignment software, software resource, sequence analysis software | Software tool based on hashing algorithm and approach to genomic reference indices from Noblis. Used to indexing genomic references. Aligns reads on reference genomes at random positions where k-mer indexes are matched with reference genomes. | Hashing algorithm, genomic reference indices, Noblis, indexing genomic reference, align reads, reference genome, random position, k-mer index, index match reference genome | Restricted | SCR_018501 | 2026-08-13 09:30:24 | 2 | |||||||||||
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Luminex: Amnis ImageStreamX Mk II System Resource Report Resource Website 100+ mentions |
Luminex: Amnis ImageStreamX Mk II System (RRID:SCR_018589) | instrument resource | Bench top multispectral imaging flow cytometer designed for the acquisition of up to 12 channels of cellular imagery. It combines per cell information with statistical significance of sample sizes of standard flow cytometry. | Benchtop Flow Cytometer, Instrument, Equipment, imaging flow cytometer, USEDit, Luminex | is listed by: USEDit | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018589.pdf | SCR_020244, SCR_020142, Model_Number_ImageStreamX_MkII | https://www.unthsc.edu/research/wp-content/uploads/sites/21/AMNIS-Imagestream.pdf | https://www.luminexcorp.com/imagestreamx-mk-ii/ | SCR_018589 | , Luminex ImageStream MkII Multispectral Imaging Flow Cytometer, MkII imaging flow cytometer, Luminex ImageStream MkII Flow Cytometer, Luminex Amnis ImageStream MkII Multispectral Imaging Flow Cytometer | 2026-08-13 09:30:14 | 133 | |||||
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ReproNim/containers Resource Report Resource Website 1+ mentions |
ReproNim/containers (RRID:SCR_018467) | narrative resource, data or information resource, software toolkit, workflow, training material, knowledge environment resource, software resource, portal | Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments. | Containerized environment, reproducible neuroimaging, ReproNim, neuroimaging, dataset, DataLad, imaging, data | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | NIBIB P41 EB019936; NSF 1429999; German Federal Ministry of Education and Research |
Free, Freely available | https://github.com/ReproNim/containers | SCR_018467 | 2026-08-13 09:30:13 | 1 |
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