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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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m6ASNP: Annotation of genetic variants by m6A function Resource Report Resource Website 1+ mentions |
m6ASNP: Annotation of genetic variants by m6A function (RRID:SCR_016048) | web service, software resource, data access protocol, software application, data analysis software, data visualization software, data processing software | Web server implemented in JAVA and PHP for annotating genetic variants by m6A function. It predicts and annotates N6-methyladenosine (m6A) alterations from genetic variants data such as germline SNPs or cancer somatic mutations. It employs two accurate prediction models for human and mouse using Random Forest algorithm. It conducts a statistical analysis for all the predicted m6A alterations. Provides statistical diagrams and a genome browser to visualize the topology characteristics of predicted m6A alterations. | N6-methyladenosine (m6A), variant annotation, effect prediction, random forest, miclip, m6a, mutant | National Key Research and Development Program 2017YFA0106700; National Natural Science Foundation of China 31771462; China Postdoctoral Science Foundation 2017M622864; Fundamental Research Funds for the Central Universities No. 17lgpy106; Guangdong Natural Science Foundation 2014TQ01R387 |
PMID:29617790 DOI:10.1093/gigascience/giy035 |
Free, Available for download, Freely available | https://github.com/RenLabBioinformatics/m6ASNP | SCR_016048 | m6ASNP | 2026-08-08 12:00:46 | 3 | |||||||
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IMAGEN Resource Report Resource Website 100+ mentions |
IMAGEN (RRID:SCR_016045) | data or information resource, consortium, project portal, portal, organization portal | Research project examining how biological, psychological, and environmental factors during adolescence may influence brain development and mental health. Using brain imaging and genetics, the project will help develop prevention strategies and improved therapies for mental health disorders in the future., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | adolescence, teen, mental, health, study, brain, development, neurological, prevention, therapy, disorder, psychology | European Commission ; Medical Research Council ; National Institute for Health Research UK ; Swedish Research Council (Vetenskapsrådet) ; German Federal Ministry of Research & Education (BMBF) ; National Institute for Health Research US ; National Institute on Drug Abuse |
PMID:21102431 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016045 | IMAGEN Consortium, IMAGEN Project, IMAGEN Study | 2026-08-08 12:00:46 | 158 | ||||||||
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Barrnap Resource Report Resource Website 500+ mentions |
Barrnap (RRID:SCR_015995) | sequence analysis software, software resource, software application, data analysis software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multithreading, fasta, sequencing, software, predict, location, ribosomal, gene, genome, RNA, prediction, bacteria, archaea, mitochondria, eukaryote, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:barrnap, OMICS_13988 | https://github.com/tseemann/barrnap, https://bio.tools/barrnap, https://sources.debian.org/src/barrnap/ | SCR_015995 | Barrnap: Basic rapid ribosomal RNA predictor | 2026-08-08 12:00:27 | 722 | |||||||
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CED: Power1401 Resource Report Resource Website 10+ mentions |
CED: Power1401 (RRID:SCR_016040) | instrument resource | Data acquisition interface from Cambridge Electronic Design Limited. Works with Spike2 to provide continuous acquisition tasks. Records waveform data, digital and marker information, and can generate waveform and digital outputs simultaneously for real-time, multi-tasking experiment control. | Cambridge Electronic Design Limited, equipment, hardware, instrument, USEDit |
is listed by: USEDit works with: Spike2 Software |
Restricted | https://drive.google.com/file/d/1fl3Sbk3t-vRgPgDNMBbZQuLSBIdJUPsO/view?usp=drivesdk | SCR_017282 | SCR_016040 | , POWER1401-3 Data Acquisition Interface, Power1401-3A, CED Power1401 3A | 2026-08-08 12:00:48 | 15 | |||||||
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BMap Resource Report Resource Website 10+ mentions |
BMap (RRID:SCR_016044) | sequence analysis software, image analysis software, software resource, software application, source code, data analysis software, alignment software, data processing software | Software that maps whole-genome and targeted bisulfite sequence reads to reference genomes. It is especially useful for reads obtained using post-bisulfite adaptor tagging (PBAT)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | mapper, whole-genome, bisulfite, sequencing, post-bisulfite, adaptor, tagging, pbat, reads, mapping | PMID:22649061 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016044 | 2026-08-08 12:00:28 | 29 | ||||||||||
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NeuroImage Field-of-View Normalization Tool Resource Report Resource Website 1+ mentions |
NeuroImage Field-of-View Normalization Tool (RRID:SCR_015957) | data or information resource, portal, topical portal | FSoftware for field-of-view normalization to minimize mismatch in different subjects' images. It aids that streamline analysis of large-scale brain MRI datasets. | normalization, fov, field, view, filed of view, brain, mri, magnetic, resonance, neuroimaging, imaging, atlas | DOI:10.1007/s12021-018-9359-z | Free, Available for download | SCR_015957 | Normalize FOV, normalizefov | 2026-08-08 12:00:27 | 4 | |||||||||
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FIONASITE Resource Report Resource Website 1+ mentions |
FIONASITE (RRID:SCR_016012) | data acquisition software, software resource, software application, data transfer software, data management software, data processing software | Software for uploading data to FIONA and capturing MR images and k-space data from medical image systems. It provides a web-interface to automate the data review (image viewer), integrate with the centralized electronic data record for assigning anonymized id's, and forward the data to the central archive. | automate, data, upload, collection, network, appliance, abcd, study | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016014, SCR_016013 | http://qi.ucsd.edu/news-article.php?id=2342&go=newer | SCR_016012 | 2026-08-08 12:00:47 | 1 | |||||||
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enroll Resource Report Resource Website 10+ mentions |
enroll (RRID:SCR_016011) | data storage software, software resource, software application, data management software, data processing software | Software which provides a framework for the secure storage of Personal Identifyable Information (PII) for a multi-site longitudinal project centrally. Used in Adolescent Brain Cognitive Development (ABCD) Study. | database, secure, framework, multisite, personal, identifiable, information, adolescence, abcd |
has parent organization: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016011 | 2026-08-08 12:00:46 | 13 | |||||||||
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Aegean Resource Report Resource Website 1+ mentions |
Aegean (RRID:SCR_015965) | sequence analysis software, software toolkit, software resource, software application, data analysis software, data processing software | Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more. | genome, evaluation, annotation, structure, loci |
is listed by: Debian is listed by: OMICtools |
National Science Foundation 1126267 | PMID:22852583 | Free, Available for download, Freely available, | OMICS_19721 | https://github.com/BrendelGroup/AEGeAn, https://sources.debian.org/src/aegean/ | SCR_015965 | AEGeAn: analysis and evaluation of genome annotations, Aegean Toolkit | 2026-08-08 12:00:45 | 9 | |||||
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Aevol Resource Report Resource Website 1+ mentions |
Aevol (RRID:SCR_015966) | software resource, software application, simulation software | Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences). | software, genetic, model, simulation, evolution, microorganism, coding, sequence, algorithm | Agence Nationale de la Recherche ANR-10-BLAN-1724; INSERM |
PMID:24278000 | Free, Available for download, Tutorial available | SCR_015966 | 2026-08-08 12:00:46 | 3 | |||||||||
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andi Resource Report Resource Website 10+ mentions |
andi (RRID:SCR_015971) | image analysis software, software resource, software application, algorithm resource, alignment software, data processing software | Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes. | algorithm, computing, estimate, analysis, genome, alignment, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Deutsche Forschungsgemeinschaft Pf672/3-1 | PMID:25504847 | Free, Freely available, Available for download | OMICS_09287, biotools:andi | https://bio.tools/andi, https://sources.debian.org/src/andi/ | SCR_015971 | 2026-08-08 12:00:46 | 41 | ||||||
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Anfo Resource Report Resource Website 1+ mentions |
Anfo (RRID:SCR_015972) | image analysis software, software resource, software application, alignment software, data processing software | Software for short read alignment and mapping of sequencing reads where the DNA sequence is somehow modified and/or there is more divergence between sample and reference than what fast mappers will handle. | alignment, program, mapper, software, sequence, DNA, ancient dna, bisulphite, treatment | Free Software Foundation ; Inc. |
Free, Available for download, Freely available | SCR_015973 | SCR_015972 | Anfo Short Read Aligner/Mapper | 2026-08-08 12:00:27 | 8 | ||||||||
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MicrobeTracker Resource Report Resource Website 100+ mentions |
MicrobeTracker (RRID:SCR_015939) | software toolkit, image analysis software, software resource, software application, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone. Software for bacterial microscopy image analysis. It is designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them. | microbe, tracking, tracker, matlab, microscopy, microbiology, bacteria, cell, cell imaging, imaging, image, analysis |
uses: MATLAB requires: MATLAB |
SCR_015939 | 2026-08-08 12:00:46 | 119 | |||||||||||
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Piggy Resource Report Resource Website 10+ mentions |
Piggy (RRID:SCR_015941) | software resource, software application, data analysis software, data processing software | Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary). | intergenic, region, bacterial, analysis, gene, genome, assembly | Medical Research Council | Free, Available for download | SCR_015941 | 2026-08-08 12:00:27 | 32 | ||||||||||
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Feeding Experimentation Device project Resource Report Resource Website 1+ mentions |
Feeding Experimentation Device project (RRID:SCR_015942) | FED | data or information resource, portal, topical portal | Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging. | Feeding, food intake, optogenetic, behavioral data analysis, data analysis software, behavior apparatus, behavior rig, reward delivery, behavior measurement, homecage, Instrument, OpenBehavior |
is listed by: OpenBehavior has parent organization: Washington University in St. Louis; Missouri; USA |
NIH | PMID:27060385 | Commercially available | https://github.com/KravitzLab/FED1, https://edspace.american.edu/openbehavior/project/feeding-experimentation-device/, https://hackaday.io/project/72964-feeding-experimentation-device-fed-20 | SCR_015942 | , FED1, FED2, Feeding Experimentation Device system, Feeding Experimentation Device | 2026-08-08 12:00:44 | 1 | |||||
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DISULFIND Resource Report Resource Website 50+ mentions |
DISULFIND (RRID:SCR_016072) | Disulfinder | sequence analysis software, software resource, software application, data analysis software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks. | predict, disulfide, bonding, state, cysteine, protein, sequence, genomic, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: University of Florence; Florence; Italy |
EU STREP APrIL II contract no. FP6-508861; EU NoE BIOPATTERN contract no. FP6-508803; Embark Fellowship from the Irish Research Council for Science ; Engineering and Technology |
PMID:16844986 DOI:10.1093/nar/gkl266 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04214, biotools:disulfind | https://bio.tools/disulfind, https://sources.debian.org/src/disulfinder/ | SCR_016072 | Cysteines Disulfide Bonding State and Connectivity Predictor | 2026-08-08 12:00:28 | 71 | ||||
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Boutiques Resource Report Resource Website 1+ mentions |
Boutiques (RRID:SCR_016073) | software toolkit, software resource, software application, software development tool, systems interoperability software | Software toolkit for a cross-platform JSON-framework for describing command-line tools and their parameters. It is accompanied by a Python tool which facilitates the creation, validation, simulation, execution, publishing, evaluation, and testing of tools described in this format. | json, standardization, interoperability, software, command, line, software containers | Free, Available for download | SCR_016073 | Boutiques Tool, Boutiques Python Tool | 2026-08-08 12:00:47 | 3 | ||||||||||
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DeepNano Resource Report Resource Website 1+ mentions |
DeepNano (RRID:SCR_016070) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software for an alternative basecaller for DNA base calling in the portable Oxford Nanopore MinION sequencing device, based on deep recurrent neural networks. Used to improve base calling accuracy and reduce sequencing error rate. | DNA, basecaller, Oxford Nanopore MinON read, sequencing, device, deep, recurrent, neural, network, accuracy, reduce, error |
is listed by: Debian is listed by: OMICtools has parent organization: Comenius University; Bratislava; Slovakia |
VEGA 1/0684/16 (BB); VEGA 1/0719/14 (TV); Slovak Research and Development Agency APVV-14-0253; NVIDIA Corporation |
PMID:28582401 | Free, Available for download | OMICS_14561 | http://compbio.fmph.uniba.sk/deepnano/, https://sources.debian.org/src/deepnano/ | SCR_016070 | DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads, DeepNano: alternative basecaller for MinION reads | 2026-08-08 12:00:47 | 5 | |||||
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statsmodel Resource Report Resource Website 100+ mentions |
statsmodel (RRID:SCR_016074) | software resource, software application, data analysis software, data processing software | Statistical software that provides classes and functions for the estimation of many different models, as well as for conducting statistical tests, and statistical data exploration. The results are tested against existing statistical packages to ensure that they are correct. http://conference.scipy.org/proceedings/scipy2010/seabold.html | python, statistic, estimate, econometric, model, library, class, function, r | Open source, Available for download | SCR_016074 | Statsmodels: Econometric and Statistical Modeling with Python | 2026-08-08 12:00:48 | 253 | ||||||||||
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Gblocks Resource Report Resource Website 1000+ mentions |
Gblocks (RRID:SCR_015945) | web application, standalone software, software resource, software application | Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | position, dna, protein, align, alignment, phylogenetic, analysis, block, ansi c, deletion, removal | is listed by: SoftCite | Fundación BBVA ; Plan Nacional de Investigación Científica BIO2002-04426-C02-02; Desarrollo e Innovación Tecnológica |
PMID:10742046 PMID:17654362 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015945 | 2026-08-08 12:00:44 | 2043 |
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