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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Drug Gene Budger Resource Report Resource Website |
Drug Gene Budger (RRID:SCR_016489) | DGB | data access protocol, service resource, software resource, web service | Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only. Application for ranking drugs to modulate specific gene based on transcriptomic signatures. | identify, drug, small, molecule, predict, influence, expression, mammalian, gene, regulate, target |
is related to: LINCS Project has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA works with: CMAP works with: Gene Expression Omnibus (GEO) |
BD2K-LINCS Data Coordination and Integration Center Mount Sinai Knowledge Management Center for IDG ; NCI U24 CA224260; NHLBI U54 HL127624 |
PMID:30169739 | Restricted | SCR_016489 | SciCrunch Registry | Drug Gene Budger | 2026-11-07 11:58:17 | 0 | ||||||
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Thermo Fisher: GeneChip™ Scanner 3000 7G Resource Report Resource Website 1+ mentions |
Thermo Fisher: GeneChip™ Scanner 3000 7G (RRID:SCR_016522) | instrument resource | Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis. | Instrument, microarray, analysis, scan, next, generation, array, whole, genome, gene, chip | Commercially available | https://drive.google.com/file/d/1du6GBtNmdw3AWBFSjRx9YQMzbZWj4uAY/view?usp=drivesdk, https://drive.google.com/file/d/1du6GBtNmdw3AWBFSjRx9YQMzbZWj4uAY/view?usp=drivesdk | https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FGSD%2FDatasheets%2Fgenechip_scanner_3000_datasheet.pdf | SCR_016522 | SciCrunch Registry | 2026-11-07 11:58:18 | 1 | |||||||||
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MorphoJ Resource Report Resource Website 10+ mentions |
MorphoJ (RRID:SCR_016483) | data analysis software, data processing software, software application, software resource, software toolkit | Software package written in Java for geometric morphometric analysis for two- and three-dimensional landmark data. Offers user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data. | geometric, morphometric, analyse, 2D, 3D, landmark, data, principal, component, discriminant, multivariate, regression, shape | has parent organization: University of Manchester; Manchester; United Kingdom | PMID:21429143 | Free, Available for download, Freely available | SCR_016483 | SciCrunch Registry | 2026-11-07 11:58:41 | 38 | |||||||||
|
Dormed Hellas: Monica AN24 Resource Report Resource Website 1+ mentions |
Dormed Hellas: Monica AN24 (RRID:SCR_016455) | instrument resource | Monitors the electrical signals on the patient’s abdomen by using the abdominal fECG and mECG wave shape to uniquely identify and separate the maternal and fetal heart rates. | Instrument, monitor, electrical, signal, patient, abdoment, separate, maternal, fetal, heart, rate | It has been discontinued | https://drive.google.com/file/d/1Agh-RBIqoW5hWevf4o9B6_dCYEUBsNH_/view?usp=sharing | https://www.accessdata.fda.gov/cdrh_docs/pdf11/K112390.pdf | SCR_016455 | SciCrunch Registry | 2026-11-07 11:58:41 | 1 | |||||||||
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Apnea, Bariatric surgery, and CPAP study Resource Report Resource Website 1+ mentions |
Apnea, Bariatric surgery, and CPAP study (RRID:SCR_016575) | ABC study | data or information resource, disease-related portal, portal, topical portal | Portal for randomized controlled trial to compare effectiveness of bariatric surgery versus continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea. Signals included in the polysomnography (PSG) montage are EEG, EMG, EOG, ECG, SpO2, airflow, CPAP pressure, CPAP flow, plethysmography, position, pulse, light, respiratory effort, snore. | dataset, bariatric, surgery, continuous, positive, airway, pressure, therapy, sleep, apnea, obesity II | is listed by: National Sleep Research Resource (NSRR) | class II obesity, obstructive sleep apnea | NHLBI K24 HL127307; NHLBI R01 HL106410 |
DOI:10.1164/rccm.201708-1637LE | Free, Available for public download, Registration required | SCR_016575 | SciCrunch Registry | and Cpap study, Bariatric surgery, Apnea | 2026-11-07 11:58:19 | 1 | |||||
|
MutaGene Resource Report Resource Website 10+ mentions |
MutaGene (RRID:SCR_016574) | data analysis software, data processing software, software application, software resource | Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity. | analyze, mutagenic, factor, turmor, decipher, cancer, genetic, heterogeneity | is listed by: OMICtools | National Library of Medicine ; NIH |
PMID:28472504 | Free, Available for download, Freely available | https://ncbiinsights.ncbi.nlm.nih.gov/tag/mutagene/ | SCR_016574 | SciCrunch Registry | 2026-11-07 11:58:42 | 10 | |||||||
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NCBI Biocollections Resource Report Resource Website 1+ mentions |
NCBI Biocollections (RRID:SCR_016459) | NCBI Biocollections | data or information resource, data processing software, database, image analysis software, organization portal, portal, registration software, software application, software resource | Registry of bio-collections linked to genomes. Collection of curated dataset of metadata for culture collections, museums, herbaria and other natural history collections, including Darwin Core institution and collection codes, and URL formulae for mapping specimen ids to web pages at the collection site. | registry, biocollection, linked, genome, dataset, metadata | SCR_016459 | SciCrunch Registry | NCBI Biocollections:National Center for Biotechnology Information Biocollections | 2026-11-07 11:58:37 | 2 | ||||||||||
|
SABRe CVD Initiative Resource Report Resource Website |
SABRe CVD Initiative (RRID:SCR_016572) | SABRe CVD | data or information resource, disease-related portal, portal, topical portal | Project to generate extensive biomarker data from Framingham Heart Study participants using immunoassays, proteomics, metabolomics/lipomics, and gene expression and microRNA profiling to advance personalized medicine through biomarker discovery and validation. | generate, biomarker, discovery, data, Framingham, Heart, Study, gene, expression, omicdata | cardiovascular disease, atherosclerosis | Free, Partially available for public, Requested authorized access | SCR_016572 | SciCrunch Registry | Systems Approach to Biomarker Research in CardioVascular Disease | 2026-11-07 11:58:38 | 0 | ||||||||
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UAMH Centre for Global Microfungal Biodiversity Resource Report Resource Website 1+ mentions |
UAMH Centre for Global Microfungal Biodiversity (RRID:SCR_016466) | biomaterial supply resource, material resource, organism supplier | Repository of microbial in Canada. Culture collection, preservation, analysis, identification of fungi living strains. Backed up by herbarium dried colonies. A reference and training centre for the identification of human and animal pathogens and allied taxa.Provides advice or assistance to projects involving fungi. | microbial, repository, collection, preservation, analysis, identification, fungi | is related to: University of Toronto; Ontario; Canada | SCR_016466 | SciCrunch Registry | 2026-11-07 11:58:41 | 5 | |||||||||||
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NRRL ARS Culture Collection Resource Report Resource Website 10+ mentions |
NRRL ARS Culture Collection (RRID:SCR_016465) | NRRL ARS | biomaterial supply resource, material resource, organism supplier | Center that collects, deposits, maintains bacteria and fungi, and facilitates microbiological research to advance agricultural production, food safety, public health, and economic development. Housed within the Mycotoxin Prevention and Applied Microbiology Research Unit at the National Center for Agricultural Utilization Research in Peoria, Illinois. | collect, deposit, maintain, facilitate, microbiology, research, agriculture, bacteria, fungi | SCR_016465 | SciCrunch Registry | NRRL:Northern Regional Research Laboratory, ARS:Agricultural Research Service | 2026-11-07 11:58:37 | 39 | ||||||||||
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1000 Fungal Genome Project Resource Report Resource Website 1+ mentions |
1000 Fungal Genome Project (RRID:SCR_016463) | data access protocol, data or information resource, database, organism-related portal, portal, project portal, software resource, topical portal, web service | Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment. | project, genomic, information, fungi, data, sequence, energy, environment |
is related to: MycoCosm is related to: Lawrence Berkeley National Laboratory has parent organization: DOE Joint Genome Institute |
the DOE Office of Biological and Environmental Research (BER) | Free, Register for an account | SCR_016463 | SciCrunch Registry | 2026-11-07 11:58:28 | 2 | |||||||||
|
MentaLiST Resource Report Resource Website 10+ mentions |
MentaLiST (RRID:SCR_016469) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. | next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools |
is listed by: bio.tools is listed by: Debian |
Canadian Institute for Health Research ; Genome BC ; Genome Canada |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | SciCrunch Registry | 2026-11-07 11:58:28 | 15 | ||||||
|
cisTEM Resource Report Resource Website 50+ mentions |
cisTEM (RRID:SCR_016502) | cisTEM | data processing software, image processing software, software application, software resource | Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. | data, processing, high, resolution, electron, cryo, macroscopy, single, particle, averaging, image, macromolecule, high, resolution, 3D, bio.tools |
is listed by: bio.tools is listed by: Debian |
Howard Hughes Medical Institute | DOI:10.7554/eLife.35383 | Open source, Trial available | biotools:cistem | https://bio.tools/cistem | SCR_016502 | SciCrunch Registry | computational imaging system for Transmission Electron Microscopy | 2026-11-07 11:58:28 | 67 | ||||
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GCTF Resource Report Resource Website 100+ mentions |
GCTF (RRID:SCR_016500) | GCTF | data analysis software, data processing software, software application, software resource | Software tool as a Graphics Processing Units (GPU) accelerated computer program for real-time contrast transfer function (CTF) determination and correction. Used for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | accurate, real, time, constrast, transfer, function, determination, correction, atomic, resolution, cryo, electron, microscopy, reconstruction, micrograph | is related to: University of Cambridge; Cambridge; United Kingdom | the Medical Research Council ; United Kingdom MC_UP_A025_1011; Wellcome Trust New Investigator Award |
PMID:26592709 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016500 | SciCrunch Registry | GContrast Transfer Function | 2026-11-07 11:58:18 | 101 | ||||||
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MIRRI Resource Report Resource Website 10+ mentions |
MIRRI (RRID:SCR_016461) | MIRRI | biobank, data access protocol, data or information resource, database, european biobank, material storage repository, organism-related portal, organization portal, portal, service resource, software resource, storage service resource, topical portal, web service | Microbial stock center. Collaborative platform for the pan-European research infrastructure for microbial resources. Provides access to microorganisms, their derivatives, associated data and services for research, development and application. | European, research, infrastructure, microbial, resource, database, service, stock, center | the European Commission 312251; the European Union’s Seventh Framework Programme 312251 |
Free, Freely available | SCR_016461 | SciCrunch Registry | Microbal Resource Research Infrastructure | 2026-11-07 11:58:17 | 11 | ||||||||
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kallisto Resource Report Resource Website 100+ mentions |
kallisto (RRID:SCR_016582) | data analysis software, data processing software, software application, software resource | Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads. | bio.tools |
is listed by: Debian is listed by: bio.tools works with: sleuth works with: kb_python |
PMID:27043002 | Free, Available for download, Freely available | biotools:kallisto | https://pachterlab.github.io/kallisto/download.html, https://bio.tools/kallisto, https://sources.debian.org/src/kallisto/ | SCR_016582 | SciCrunch Registry | kallisto v0.43.1 | 2026-11-07 11:58:19 | 148 | ||||||
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Global Catalogue of Microorganisms Resource Report Resource Website 1+ mentions |
Global Catalogue of Microorganisms (RRID:SCR_016460) | GCM | data or information resource, database, organism-related portal, portal, topical portal | Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information. | research, deep, mining, genomic, data, retrival, analysis, visualisation, , microbial, resource, | the 13th Five-year Informatization Plan of the Chinese Academy of Sciences ; the Bureau of International Cooperation of the Chinese Academy of Sciences ; the National Key Research Program of China ; the National Science Foundation for Young Scientists of China ; the Strategic Priority Research Program of the Chinese Academy of Sciences |
PMID:29718202 | Free, Available to the scientific and industrial communities | r3d100010696 | https://doi.org/10.17616/R3J315 | SCR_016460 | SciCrunch Registry | GCM:Global Catalogue of Microorganisms | 2026-11-07 11:58:41 | 5 | |||||
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Prodigal Resource Report Resource Website 1000+ mentions |
Prodigal (RRID:SCR_011936) | Prodigal | simulation software, software application, software resource | Software tool for protein coding gene prediction for prokaryotic genomes. |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: Oak Ridge National Laboratory |
PMID:20211023 | Free, Available for download, Freely available | SCR_021246, OMICS_01493 | https://sources.debian.org/src/prodigal/ | http://prodigal.ornl.gov/ | SCR_011936 | SciCrunch Registry | , PROkaryotic DYnamic programming Gene-finding ALgorithm, Prokaryotic Dynamic Programming Genefinding Algorithm | 2026-11-07 11:57:30 | 3398 | |||||
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Oases Resource Report Resource Website 100+ mentions |
Oases (RRID:SCR_011896) | Oases | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. | bio.tools, transcriptome assembler |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
DOI:10.1093/bioinformatics/bts094 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01322, biotools:oases | https://bio.tools/oases | https://sources.debian.org/src/oases/ | SCR_011896 | SciCrunch Registry | 2026-11-07 11:57:22 | 289 | |||||
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Rnnotator Resource Report Resource Website 10+ mentions |
Rnnotator (RRID:SCR_011897) | Rnnotator | software resource | Software designed to assemble Illumina single or paired-end reads. |
is listed by: OMICtools has parent organization: Brown University; Rhode Island; USA |
OMICS_01323 | SCR_011897 | SciCrunch Registry | 2026-11-07 11:57:23 | 24 |
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