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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Image Registration Toolkit Resource Report Resource Website 10+ mentions |
Image Registration Toolkit (RRID:SCR_000067) | IRTK, MIRTK | software toolkit, image processing software, image analysis software, data processing software, software application, software resource | Software image processing toolkit. Provides collection of libraries and command-line tools to assist in processing and analyzing imaging data. Used for adult and neonatal brain MR image registration, including rigid, affine, and non-rigid transformations, as well as reconstruction of cortical surface meshes. | image processing, processing and analyzing imaging data, adult and neonatal brain MR image registration, | has parent organization: Imperial College London; London; United Kingdom | PMID:10534053 | Free, Available for download, Freely available | nlx_155983 | https://github.com/BioMedIA/MIRTK | http://www.doc.ic.ac.uk/~dr/software/ | SCR_000067 | Medical Image Registration ToolKit | 2026-08-15 11:21:41 | 15 | ||||
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Pharmaceuticals and Medical Devices Agency Resource Report Resource Website 1+ mentions |
Pharmaceuticals and Medical Devices Agency (RRID:SCR_000244) | PMDA | commercial organization | A Japanese regulatory government agency which regulates the safety, efficacy and quality of pharmaceuticals and medical devices in order to protect the public health of the people. The agency plays three main roles: drug and medical device testing, post-marketing drug safety, and victim compensation for those affected by adverse drug reactions from pharmaceuticals or other biological products. It is an incorporated administrative agency with non-civil service status. | government, public health, pharmaceutical, medical devices, victim compensation, medical device testing, post-marketing, drug safety | is related to: Predictive Safety Testing Consortium | grid.490702.8, nlx_157922, Wikidata: Q932661, ISNI: 417639556 | https://ror.org/03mpkb302 | SCR_000244 | Japanese Pharmaceuticals and Medical Devices Agency, Pharmaceuticals and Medical Devices Agency - Japan, Pharmaceuticals and Medical Devices Agency Japan | 2026-08-15 11:21:42 | 1 | |||||||
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Cistrome Resource Report Resource Website 10+ mentions |
Cistrome (RRID:SCR_000242) | data access protocol, software resource, web service | Web based integrative platform for transcriptional regulation studies. | Transcriptional, regulation, Chip, data, analysis, genome, gene, expression, motif, mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy has parent organization: Harvard University; Cambridge; United States |
Dana-Farber Cancer Institute High Tech and Campaign Technology Fund ; National Basic Research Program of China ; NHGRI HG004069; NIDDK DK074967; NIDDK DK062434 |
PMID:21859476 | Free, Freely available | SCR_017663, biotools:cistrome, OMICS_02173 | http://cistrome.org/ap/root, https://bio.tools/cistrome | SCR_000242 | Galaxy Cistrome | 2026-08-15 11:21:45 | 17 | |||||
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TAPIR: target prediction for plant microRNAs Resource Report Resource Website 10+ mentions |
TAPIR: target prediction for plant microRNAs (RRID:SCR_000237) | TAPIR | Web server designed for prediction of plant microRNA targets. | prediction of plant microRNA targets, microrna, target, fasta, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium has parent organization: VIB; Flanders; Belgium |
PMID:20430753 | biotools:tapir, OMICS_04004 | https://bio.tools/tapir | SCR_000237 | 2026-08-15 11:21:45 | 10 | ||||||||
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Surflex-Dock Resource Report Resource Website 1+ mentions |
Surflex-Dock (RRID:SCR_000196) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software program that screens large libraries of compounds including ligands, and their docking. | ligand docking, library, compound, compound library | is listed by: OMICtools | PMID:22569590 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01607 | SCR_000196 | 2026-08-15 11:21:44 | 6 | ||||||||
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Evernote Resource Report Resource Website 1+ mentions |
Evernote (RRID:SCR_000198) | Evernote | software application, authoring tool, software resource | A note taking software that synchronizes information such as notes, web clips, audio files, photos and video collected across multiple devices. It allows for easy sharing and collaboration on projects. | note taking, web clips, audio, video collection, audio, collaboration | is listed by: FORCE11 | Free, Available for download, Freely available | nlx_149450 | SCR_000198 | 2026-08-15 11:21:41 | 4 | ||||||||
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MetaDE Resource Report Resource Website 1+ mentions |
MetaDE (RRID:SCR_000199) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. Software package that implements 12 major meta-analysis methods for differential expression analysis.Package was removed from the CRAN repository.Formerly available versions can be obtained from the archive.Archived on 2018-01-23 as check problems were not corrected in time. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:22863766 | Free, Available for download, Freely available | OMICS_04033 | http://cran.r-project.org/web/packages/MetaDE/ | SCR_000199 | MetaDE: Microarray meta-analysis for differentially expressed gene detection | 2026-08-15 11:21:44 | 1 | ||||||
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SODOCK Resource Report Resource Website 1+ mentions |
SODOCK (RRID:SCR_000193) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems. | particle swarm optimization, protein, ligand, docking, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
PMID:17186483 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:sodock, OMICS_01606 | https://bio.tools/sodock | SCR_000193 | 2026-08-15 11:21:41 | 1 | |||||||
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Sanjeevini Resource Report Resource Website 1+ mentions |
Sanjeevini (RRID:SCR_000191) | production service resource, web service, data access protocol, software resource, service resource, analysis service resource | A complete drug designing software suite with an accessible web-server for targeted directed lead molecule discovery. | drug design, molecule discovery, ligand, protein, DNA, metalloproteinase, docking, protein-ligand complex, bioinformatics | is listed by: OMICtools | PMID:23282245 | Public, Open Source | OMICS_01605 | SCR_000191 | 2026-08-15 11:21:44 | 1 | ||||||||
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UnSplicer Resource Report Resource Website 1+ mentions |
UnSplicer (RRID:SCR_000226) | software resource | An RNA-seq alignment program that provides alignment of short reads to a reference genome. The program requires two inputs that are provided by the output of GeneMark-ES: HMM model parameters and ab initio gene predictions. UnSplicer is a sister pipeline to TrueSight. | RNA, sequencing, alignment, short reads, genome, genemark-es, gene prediction |
is listed by: OMICtools has parent organization: Georgia Institute of Technology; Georgia; USA |
PMID:24259430 | Free, Available for download, Freely available | OMICS_01806 | SCR_000226 | 2026-08-15 11:21:45 | 1 | ||||||||
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ChromasPro Resource Report Resource Website 10+ mentions |
ChromasPro (RRID:SCR_000229) | data processing software, software application, software resource, data acquisition software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31,2023. Software which is able to assemble data from 454 and Illumina next-generation sequencers, with up to 100,000 sequences if 2 Gb RAM is available. | genome, sequence, dna, assemble, data, illumina, next gen sequence, next generation | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01808 | SCR_000229 | 2026-08-15 11:21:42 | 14 | ||||||||||
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RNAmotifs Resource Report Resource Website 1+ mentions |
RNAmotifs (RRID:SCR_000263) | RNAmotifs | software resource | Software that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs. | rna, motif |
is listed by: OMICtools has parent organization: Bitbucket |
OMICS_02287 | https://bitbucket.org/rogrro/rna_motifs | SCR_000263 | rna_motifs, rna motifs | 2026-08-15 11:21:42 | 1 | |||||||
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University of Texas Medical Branch at Galveston Resource Report Resource Website 1+ mentions |
University of Texas Medical Branch at Galveston (RRID:SCR_000144) | UTMB | university | A division of the University of Texas that is dedicated to medical education. | texas, medical, university, medical education |
is related to: Clinical and Translational Science Awards Consortium has parent organization: University of Texas System; Texas; USA is parent organization of: Mexican Health and Aging Study is parent organization of: University of Texas Tumor Bank is parent organization of: Longitudinal Study of Elderly Mexican American Health is parent organization of: UTMB Mass Spectrometry Core is parent organization of: University of Texas Medical Branch at Galveston Labs and Facilities |
Wikidata: Q921264, grid.176731.5, Crossref funder ID: 100008013, nlx_69430, ISNI: 0000 0001 1547 9964 | https://ror.org/016tfm930 | SCR_000144 | University of Texas Medical Branch, UT Medical Branch, UT Medical Branch at Galveston, University of Texas Medical Branch at Galveston | 2026-08-15 11:21:41 | 1 | |||||||
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CommonMind Consortium Resource Report Resource Website 1+ mentions |
CommonMind Consortium (RRID:SCR_000139) | CommonMind | data or information resource, portal, topical portal | Sage Bionetworks, Mount Sinai School of Medicine (MSSM), University of Pennsylvania (Penn), the National Institute of Mental Health (NIMH), and Takeda Pharmaceuticals Company Limited (TAKEDA) have launched a Public-Private Pre-Competitive Consortium, the CommonMind Consortium, to generate and analyze large-scale genomic data from human subjects with neuropsychiatric disease and to make this data and the associated analytical results broadly available to the public. This collaboration brings together disease area expertise, large scale and well curated brain sample collections, and data management and analysis expertise from the respective institutions. As many as 450 million people worldwide are believed to be living with a mental or behavioral disorder: schizophrenia and bipolar disorder are two of the top six leading causes of years lived with disability according to the World Health Organization. The burden on the individual as well as on society is significant with estimates for the health care costs for these individuals as high as four percent GNP. This highlights a grave need for new therapies to alleviate this suffering. Researchers from MSSM including Dr. Pamela Sklar, Dr. Joseph Buxbaum and Dr. Eric Schadt will join with Dr. Raquel Gur and Dr. Chang-Gyu Hahn from Penn to combine their extensive brain bank collections for the generation of whole genome scale RNA and DNA sequence data. Dr.Pamela Sklar, Professor of Psychiatry and Neuroscience at MSSM commented this is an exciting opportunity for us to use the newest genomic methods to really expand our understanding of the molecular underpinnings of neuropsychiatric disease, while Dr Raquel Gur, Professor of Psychiatry from Penn observed this will be a great complement to some of the large-scale genetic analyses that have been carried out to date because it will give a more complete mechanistic picture. The CommonMind Consortium is committed to generating an open resource for the community and invites others with common goals to contact us at info (at) CommonMind.org. | molecular data, neuropsychiatric disease, human, data, brain bank, brain, dna, rna | has parent organization: Sage Bionetworks | Neuropsychiatric disease | Sage Bionetworks ; Mount Sinai School of Medicine; New York; USA ; University of Pennsylvania; Pennsylvania; USA ; Takeda ; NIMH |
nlx_144615 | http://commonmind.org/WP/ | SCR_000139 | 2026-08-15 11:21:43 | 4 | ||||||
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Polytechnic University of Madrid; Madrid; Spain Resource Report Resource Website 1+ mentions |
Polytechnic University of Madrid; Madrid; Spain (RRID:SCR_000253) | UPM | university | A public technical university in Madrid with progams at the undergraduate, graduate and postdoctorate level in fields such as architecture and mining in addition to engineering in areas including forestry, agriculture, computer science and aeronautics. | engineering, civil, aeronautic, computer science, agriculture, forestry, mining, architecture, mathematics, technical |
is parent organization of: DIStributions of SPINEs is parent organization of: BioInformatics Resource Inventory is parent organization of: HERMES |
nlx_35130 | SCR_000253 | Universidad Politecnica de Madrid, Polytechnic University of Madrid, Technical University of Madrid, Universidad Politécnica de Madrid | 2026-08-15 11:21:45 | 1 | ||||||||
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Polish Academy of Sciences Poznan; Poznan; Poland Resource Report Resource Website 1+ mentions |
Polish Academy of Sciences Poznan; Poznan; Poland (RRID:SCR_000248) | institution | An academy of sciences that is based in Poland. The academy is an important institution for the development of science research in Poland, in addition to being part of a larger network of research institutes. | academy of sciences, research institute, poland, science research |
is parent organization of: genes2mind is parent organization of: RNA FRABASE - RNA FRAgments search engine and dataBASE is parent organization of: Aminoacyl-tRNA synthetase database |
nlx_11309 | http://www.pan.poznan.pl/ | SCR_000248 | PAN | 2026-08-15 11:21:45 | 1 | ||||||||
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miRanalyzer Resource Report Resource Website 1+ mentions |
miRanalyzer (RRID:SCR_000163) | web application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. A microRNA detection and analysis tool for next-generation sequencing experiments. The program uses a minimum match length of 17bp starting at the first base of the read. The maximum read length is set to 28bp. Reads with more than 5 matches to the genome are discarded, and if a read matches to more than 5 transcripts or Rfam entries it will be removed. | mirna, microrna, next gen sequencing, analysis, next generation, next gen, detection tool, analysis tool | is listed by: OMICtools | PMID:21515631 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00361 | SCR_000163 | 2026-08-15 11:21:41 | 8 | ||||||||
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Grinder Resource Report Resource Website 1+ mentions |
Grinder (RRID:SCR_000168) | Grinder | software resource | An open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. The tool is available through multiple interfaces like GUI, CLI and API. It is useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities. | simulation, amplicon, shotgun, genomic sequencing, clinical, metagenomic, transcriptomic and metatranscriptomic |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:22434876 DOI:10.1093/nar/gks251 |
Free, Available for download, Freely available | OMICS_01508 | https://sources.debian.org/src/grinder/ | SCR_000168 | 2026-08-15 11:21:41 | 3 | ||||||
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CNTools Resource Report Resource Website 1+ mentions |
CNTools (RRID:SCR_000281) | CNTools | software resource | Software package that provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data. | copy number variation, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02061 | SCR_000281 | CNTools - Convert segment data into a region by sample matrix to allow for other high level computational analyses | 2026-08-15 11:21:46 | 1 | |||||||
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Queens University Belfast; Ireland; United Kingdom Resource Report Resource Website 1+ mentions |
Queens University Belfast; Ireland; United Kingdom (RRID:SCR_000279) | Queen's | university | A public research university in Belfast, Ireland that offers degree programs in a wide variety of disciplines at the undergraduate, graduate and postgraduate level. | public, research, ireland, belfast |
is related to: International AMD Genetics Consortium is parent organization of: Northern Ireland Virtual Tissue Archive is parent organization of: QuPath |
Wikidata:Q877925, grid.4777.3, nlx_143527, Crossref funder ID:501100000873, ISNI:0000 0004 0374 7521 | https://ror.org/00hswnk62 | SCR_000279 | Queen's University Belfast | 2026-08-15 11:21:42 | 1 |
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