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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CRISPR-P Resource Report Resource Website 10+ mentions |
CRISPR-P (RRID:SCR_016941) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment. | synthetic, single, RNA, CRISP, plant, Cas9, target, DNA, sequence, analysis, restriction, enzyme, sgRNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
Fundamental Research Funds for the Central Universities ; National Basic Research Program of China ; Program for New Century Excellent Talents in University |
PMID:24719468 | Free, Freely available | biotools:CRISPR-P | https://bio.tools/CRISPR-P | SCR_016941 | CRISPR-P 2.0, Clustered Regularly Interspaced Short Palindromic Repeats P, CRISPR P | 2026-09-19 12:53:31 | 42 | |||||
|
MacroModel Resource Report Resource Website 100+ mentions |
MacroModel (RRID:SCR_016747) | simulation software, software application, software resource | Software package for molecular modeling. Computes free energy changes using free energy perturbation method. Used to examine molecular conformations, molecular motion, and intermolecular interactions, such as those in a ligand-receptor complex. | molecular, modeling, free, energy, changes, perturbation, method, conformation, motion, interaction, ligand, receptor, complex | has parent organization: Schrodinger | Commercially available, Free version available | https://en.freedownloadmanager.org/Windows-PC/MacroModel.html | SCR_016747 | 2026-09-19 12:53:28 | 138 | |||||||||
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ascat Resource Report Resource Website 10+ mentions |
ascat (RRID:SCR_016868) | ASCAT | data analysis software, data processing software, software application, software resource | Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data. | allele, specific, copy, number, analysis, tumor, purity, ploidy, sequencing, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:20837533 | Free, Available for download, Freely available | BioTools:ascat, biotools:ascat | https://github.com/VanLoo-lab/ascat, https://www.crick.ac.uk/research/labs/peter-van-loo/software, https://bio.tools/ascat, https://sources.debian.org/src/r-other-ascat/ | SCR_016868 | ASCAT 3.0, ASCAT 2.0, ASCAT 4.0, ASCAT 1.0, Allele-Specific Copy Number Analysis of Tumors, Allele Specific Copy Number Analysis of Tumors | 2026-09-19 12:53:29 | 42 | |||||
|
EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | data processing software, image processing software, software application, software resource | Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography. | image, processing, data, transmission, electron, microscope, single, particle, reconstruction, helical, 2D, whole, cell, tomography, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
NIH | PMID:16859925 | Free, Available for download, Freely available | biotools:eman | https://bio.tools/eman | https://blake.bcm.edu/emanwiki/EMAN1 | SCR_016867 | EMAN1, EMAN2 | 2026-09-19 12:53:29 | 107 | |||
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Pyclone Resource Report Resource Website 10+ mentions |
Pyclone (RRID:SCR_016873) | data analysis software, data processing software, software application, software resource | Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing. | infer, prevalence, point, mutation, heterogeneous, cancer, probabilistic, population, NGS, sequencing, data, analysis | PMID:24633410 | Available for download, Free for academic, nonprofit use | https://bitbucket.org/aroth85/pyclone/wiki/Home | SCR_016873 | PyClone | 2026-09-19 12:53:30 | 46 | ||||||||
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Shape screening Resource Report Resource Website 1+ mentions |
Shape screening (RRID:SCR_016750) | simulation software, software application, software resource | Software tool for shape-based superposition and similarity searching. Identifies new compounds with shapes (and, if desired, other properties) that are similar to the known binder. | shape, based, superposition, search, new, compound | has parent organization: Schrodinger | Commercially available | SCR_016750 | 2026-09-19 12:53:28 | 3 | ||||||||||
|
Metab Resource Report Resource Website 1+ mentions |
Metab (RRID:SCR_016877) | Metab | data analysis software, data processing software, software application, software resource, software toolkit | Software package as a metabolomic data processing pipeline in R codes. | metabolomic, data, processing, pipeline, analysis, datasets | Health Research Council of New Zealand | DOI:10.1093/bioinformatics | Free, Available for download, Freely available | https://bioconductor.org/packages/release/bioc/html/Metab.html | SCR_016877 | Metabolome, Metab 1.0 | 2026-09-19 12:53:30 | 1 | ||||||
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OpenBMI Resource Report Resource Website 1+ mentions |
OpenBMI (RRID:SCR_016876) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software package for the development of Brain-Computer Interfaces with advanced pattern recognition algorithms. Used for analyzing brain signals which can be used to acquire, filter, process, classify and visualize brain signals in real time. | brain, computer, interface, analysis, signal, acquire, filter, process, visualize, data | has parent organization: Korea University; Seoul; South Korea | Free, Available for download, Freely available | http://openbmi.org/ | SCR_016876 | 2026-09-19 12:53:30 | 5 | |||||||||
|
BioNano: Irys system Resource Report Resource Website 10+ mentions |
BioNano: Irys system (RRID:SCR_016754) | instrument resource | System by BioNano Genomics ( formerly BioNanomatrix) which provides optical next generation mapping (NGM). Used for sequence assembly and structural variation analysis. Provides Scaffold Bionano genome mapping data with sequencing data to improve assembly contiguity, reduce sequencing coverage needed, and automatically correct errors in sequencing based assemblies. | instrument, Irys, system, BioNano Genomics, BioNanomatrix, optical, next, generation, mapping, sequence, assembly, structural, variation, analysis, data, | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_016754.pdf | https://bionanogenomics.com/wp-content/uploads/2017/01/2016-Irys-System-Brochure.pdf | https://bionanogenomics.com/technology/genome-assembly/ | SCR_016754 | 2026-09-19 12:53:28 | 35 | ||||||||
|
KnowEnG Resource Report Resource Website 1+ mentions |
KnowEnG (RRID:SCR_016875) | data or information resource, organization portal, portal, software resource, training resource | Part of the NIH Big Data to Knowledge (BD2K) Initiative. One of 11 Centers of Excellence in Big Data Computing. Platform for genomics data analysis where user-supplied data sets will be analyzed in the context of existing knowledge. E-science framework for genomics where biomedical scientists will have access to powerful methods of data mining, network mining, and machine learning to extract knowledge out of genomics data. | center, excellence, big, data, computing, biomedical, analytics |
has parent organization: Mayo Clinic has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NIGMS U54 GM114838 | PMID:26205246 | https://github.com/BD2K/KnowEng | SCR_016875 | Knowledge Engine for Genomics, The Knowledge Engine for Genomics | 2026-09-19 12:53:30 | 1 | |||||||
|
Phenograph Resource Report Resource Website 100+ mentions |
Phenograph (RRID:SCR_016919) | PhenoGraph | data analysis software, data processing software, software application, software resource | Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity. | high, dimention, single, cell, data, phenotype, analysis, heterogeneity |
uses: Python Programming Language is related to: Rphenograph |
CIRM DR1 01477; CIRM RB201592; Entertainment Industry Foundation ; NCI P01 CA034233; NCI R01 CA130826; NCI R01 CA164729; NCI U54 CA121852; NCI U54 CA143907; NCI U54 CA149145; NIAID U19 AI057229; NICHD DP1 HD084071; NIGMS R00 GM104148; NIH Office of the Director DP2 OD002414; NIH N01 HV00242; Packard Fellowship for Science and Engineering ; Rachford and Carlota Harris Endowed Professorship ; Stand Up To Cancer Phillip A. Sharp Award SU2CAACRPS04; US Department of Health and Human Services HHSN272200700038C; US DOD W81XWH1210591; US FDA HHSF223201210194C |
PMID:26095251 | Free, Available for download, Freely available | https://github.com/JinmiaoChenLab/Rphenograph | https://github.com/jacoblevine/PhenoGraph | SCR_016919 | 2026-09-19 12:53:30 | 235 | |||||
|
ENteric Immunity SImulator (ENISI) Multi scale model Resource Report Resource Website 1+ mentions |
ENteric Immunity SImulator (ENISI) Multi scale model (RRID:SCR_016918) | ENISI MSM | acknowledgement required, data or information resource, narrative resource, simulation software, software application, software repository, software resource, source code, unspecified license | Software tool for simulating the mucosal immune responses to Helicobacter pylori infection in stomach. | simulation, prediction, mucosal, immune, response, Helicobacter Pylori, infection, stomach | Defense Threat Reduction Agency HDTRA11810008; Nutritional Immunology and Molecular Medicine Laboratory |
Free, Available for download, Freely available | SCR_016918 | ENteric Immunity SImulator Multi Scale Model | 2026-09-19 12:53:30 | 1 | ||||||||
|
clusterProfiler Resource Report Resource Website 10000+ mentions |
clusterProfiler (RRID:SCR_016884) | data analysis software, data processing software, data visualization software, software application, software resource | Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters. | data, statistical, analysis, visualization, gene, cluster, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
2007 Chang-Jiang Scholars Program ; Fundamental Research Funds for the Central Universities ; Guangdong Natural Science Research Grant ; National 973 Projects of China ; National Natural Science Foundation of China |
PMID:22455463 | Free, Available for download, Freely available | biotools:clusterprofiler | https://github.com/GuangchuangYu/clusterProfiler, https://guangchuangyu.github.io/software/clusterProfiler/, https://bio.tools/clusterprofiler | SCR_016884 | Cluster Profiler | 2026-09-19 12:53:30 | 13465 | |||||
|
CheckMyMetal Resource Report Resource Website 1+ mentions |
CheckMyMetal (RRID:SCR_016887) | CMM | data access protocol, software resource, web service | Metal binding site validation server. Used for systematic inspection of the metal-binding architectures in macromolecular structures. The validation parameters that CMM examines cover the entire binding environment of the metal ion, including the position, charge and type of atoms and residues surrounding the metal. | metal, binging, site, validation, server, systematic, inspection, macromolecular, structure, ion, charge, position, atom | NHGRI HG008424; NIAID HHSN272201200026C; NIGMS GM117325 |
PMID:28291757 | Free, Freely available | SCR_016887 | 2026-09-19 12:53:30 | 8 | ||||||||
|
Kidney Precision Medicine Project Resource Report Resource Website 50+ mentions |
Kidney Precision Medicine Project (RRID:SCR_016920) | KPMP | availability annotation standard, consortium, data or information resource, disease-related portal, narrative resource, nif annotation standard, organization portal, portal, project portal, standard specification, the community can contribute to this resource, topical portal | Project to ethically obtain and evaluate human kidney biopsies from participants with Acute Kidney Injury (AKI) or Chronic Kidney Disease (CKD), create a kidney tissue atlas, define disease subgroups, and identify critical cells, pathways, and targets for novel therapies. Used to develop the next generation of software tools to visualize and understand the various components of kidney diseases and to optimize data collection. Multi site collaboration comprised of patients, clinicians, and investigators from across the United States. | ethically, obtain, evaluate, human, kidney, biopsy, collaboration, patient, clinician, researcher, acute, injury, chronic, disease, tissue, atlas, cell, pathway, target, novel, therapy, data, collection |
is listed by: NIDDK Information Network (dkNET) is related to: Kidney Tissue Atlas |
Acute Kidney Injury, Chronic Kidney Disease | NIDDK | Open resource for academics, industry, and the broader scientific community | SCR_016920 | Kidney Precision Medicine Project, The Kidney Precision Medicine Project | 2026-09-19 12:53:30 | 72 | ||||||
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Bestus Bioinformaticus Duk Resource Report Resource Website 100+ mentions |
Bestus Bioinformaticus Duk (RRID:SCR_016969) | BBDuk | data analysis software, data analytics software, data processing software, software application, software resource | Software tool for trimming and filtering sequencing data. Used to combine data quality related trimming, filtering, and masking operations into a single tool adapter. BBDuk2 allows multiple kmer based operations in a single pass. | sequencing, data, quality, trimming, filtering, masking, operation, single, tool, adapter, contaminant, sequence, GC, length, entropy, format, conversion, histogram, kmer, estimation, decontamination |
is listed by: Bestus Bioinformaticus Tools has parent organization: DOE Joint Genome Institute works with: Reformat |
http://seqanswers.com/forums/showthread.php?t=42776, https://www.geneious.com/plugins/bbduk/#links | SCR_016969 | BB Duk, Decontamination Using Kmers, Bestus Bioinformaticus Decontamination using kmers, BBDuk2, BBDUK, BBDuk, BBDuk 2, Bestus Bioinformaticus Decontamination Using kmers | 2026-09-19 12:53:31 | 212 | ||||||||
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PICRUSt Resource Report Resource Website 10+ mentions |
PICRUSt (RRID:SCR_016855) | PICRUSt | simulation software, software application, software resource | Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome. | predict, metagenome, functional, content, DNA, sample, marker, gene, sequence, data, microbiome, 16S, RNA | is related to: PICRUSt2 | ARO W911NF1110473; Canada Research Chairs program ; Canadian Institutes of Health Research ; Crohn’s and Colitis Foundation of America ; Howard Hughes Medical Institute ; NHGRI R01 HG004872; NHGRI R01 HG005969; NHGRI U01 HG004866; NIDDK P01 DK078669; NSF CAREER DBI1053486; Sloan Foundation |
PMID:23975157 | Free, Available for download, Freely available | SCR_016856 | SCR_016855 | Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt | 2026-09-19 12:53:29 | 45 | |||||
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QuickNII Resource Report Resource Website 10+ mentions |
QuickNII (RRID:SCR_016854) | QuickNII | data processing software, image analysis software, image processing software, registration software, software application, software resource | Histological brain section series aligner to volumetric atlases. Software tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems. Part of the QUINT workflow. | section, series, aligner, volumetric, 3D, atlas, reference, space, anchoring, data, image, microscopic, standardized, coordinate, system, bio.tools |
is used by: BICCN is listed by: Debian is listed by: bio.tools is listed by: EBRAINS is related to: LocaliZoom is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway |
European Union Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement | PMID:31141518 | Free, Available for download, Freely available | biotools:QuickNII | https://quicknii.readthedocs.io; https://bio.tools/QuickNII, https://github.com/Tevemadar/QuickNII | SCR_016854 | 2026-09-19 12:53:29 | 42 | |||||
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University of Muenster; Muenster; Germany Resource Report Resource Website |
University of Muenster; Muenster; Germany (RRID:SCR_016853) | data or information resource, portal, topical portal | The University of Münster is a public university located in the city of Münster, North Rhine-Westphalia in Germany. It is Germany fifth largest university. | institution, university, Germany, public | is parent organization of: NanoPipe | SCR_016853 | The University of Münster | 2026-09-19 12:53:29 | 0 | ||||||||||
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Signal Resource Report Resource Website 10+ mentions |
Signal (RRID:SCR_017081) | data acquisition software, data analysis software, data processing software, software application, software resource | Software package for sweep based data acquisition and analysis of time based waveform data obtained through CED digital analogue converter by Cambridge Electronic Design System Limited. Used for transient capture, patch and voltage clamp, LTP studies, evoked response and TMS. | sweep, based, data, acquisition, analysis, time, based, waveform, data, CED, transient, capture, patch, voltage, clamp, LTP study, evoked, response | Available for purchase | SCR_017081 | Signal Version 6, CED Signal, Cambridge Electronic Design Signal | 2026-09-19 12:53:34 | 13 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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