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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Phyre Resource Report Resource Website 500+ mentions |
Phyre (RRID:SCR_010270) | algorithm | A structure prediction system to reliably detect remote homologies. | has parent organization: Imperial College London; London; United Kingdom | PMID:19247286 | nlx_156932 | SCR_010270 | Protein Homology/Anology Recognition Engine | 2026-08-01 12:04:11 | 665 | |||||||||
|
BIOBASE Corporation Resource Report Resource Website 100+ mentions |
BIOBASE Corporation (RRID:SCR_010271) | commercial organization | THIS RESOURCE IS OUT OF SERVICE, documented on February 1st,2022. BIOBASE offers academic and non-profit organizations free access to TRANSFAC?? non-professional version with much reduced functionality and content compared to our professional database. | FASEB list |
is related to: Human Gene Mutation Database is parent organization of: Genome Trax is parent organization of: TRANSPATH is parent organization of: Gene Regulation Programs is parent organization of: TRANSCompel is parent organization of: Gene Regulation Databases |
THIS RESOURCE IS OUT OF SERVICE | nlx_156933 | SCR_010271 | 2026-08-01 12:04:07 | 183 | |||||||||
|
BitSeq Resource Report Resource Website 10+ mentions |
BitSeq (RRID:SCR_009904) | BitSeq | software resource | A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/btv483 DOI:10.1093/bioinformatics/bts260 |
, OMICS_01269, biotools:bitseq | https://bio.tools/bitseq, https://sources.debian.org/src/bitseq/, | SCR_009904 | 2026-08-01 12:04:11 | 19 | |||||||
|
U.S. Department of Labor Resource Report Resource Website 1+ mentions |
U.S. Department of Labor (RRID:SCR_010157) | DOL | institution | Fosters, promotes, and develops the welfare of the wage earners, job seekers, and retirees of the United States; improves working conditions; advances opportunities for profitable employment; and assures work-related benefits and rights. | grid.420412.1, nlx_151864, ISNI: 0000 0001 2097 824X, Wikidata: Q628807, Crossref funder ID: 100000778 | https://ror.org/05mbkbj54 | SCR_010157 | US Dept. of Labor, US DOL, US Department of Labor, United States Department of Labor | 2026-08-01 12:04:11 | 1 | |||||||||
|
Johns Hopkins University; Maryland; USA Resource Report Resource Website 10+ mentions |
Johns Hopkins University; Maryland; USA (RRID:SCR_010247) | JHU | university | Johns Hopkins University is private research university in Baltimore, Maryland. Founded in 1876, university was named for its first benefactor, American entrepreneur, abolitionist, and philanthropist Johns Hopkins. | private, university, Baltimore, Maryland |
uses: DIRECT2experts is affiliated with: Diabetes Research Centers is related to: Alzheimers Disease Genetics Consortium is related to: International AMD Genetics Consortium is related to: ABX Guide is related to: Clinical and Translational Science Awards Consortium is parent organization of: SynaptomeDB is parent organization of: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA is parent organization of: sim4cc is parent organization of: MRI Studio is parent organization of: CKID A Prospective Cohort Study of Kidney Disease in Children is parent organization of: Nonalcoholic Steatohepatitis Clinical Research Network is parent organization of: ASprofile is parent organization of: GlimmerHMM is parent organization of: Neurogenetics and Behavior Center is parent organization of: Human Proteinpedia is parent organization of: Schramm Lab Spinal Cord Atlases is parent organization of: NetPath is parent organization of: Academic Drug Discovery Consortium is parent organization of: CardioVascular Research Grid (CVRG) is parent organization of: Johns Hopkins University; Undergraduate Neuroscience Program is parent organization of: Bowtie is parent organization of: FLASH is parent organization of: TMAJ is parent organization of: Gastroparesis Clinical Research Consortium is parent organization of: HPRD - Human Protein Reference Database is parent organization of: Atlweb: Alternatives to Animal Testing is parent organization of: Center for Inherited Disease Research is parent organization of: The Protein Coil Library is parent organization of: HIV Guide is parent organization of: Johns Hopkins School of Medicine Department of Molecular and Comparative Pathobiology is parent organization of: Classic Articles in Visual Perception is parent organization of: Experimental Man Blog is parent organization of: MYC Cancer Gene is parent organization of: JIST: Java Image Science Toolkit is parent organization of: DOTS WM tract segmentation is parent organization of: JHU Proj. in Applied Medical Imaging is parent organization of: LDDMM is parent organization of: Johns Hopkins Bloomberg School of Public Health; Maryland; USA is parent organization of: Genetic Resources Core Facility is parent organization of: LS-SNP/PDB is parent organization of: JHU Deep Sequencing and Microarray Core is parent organization of: Glimmer is parent organization of: Johns Hopkins University Labs and Facilities is parent organization of: CRAVAT is parent organization of: John Hopkins University, In-Vivo Cellular Molecular Imaging Center is parent organization of: RosettaDock is parent organization of: CoGAPS is parent organization of: Blox is parent organization of: National Resource for Quantitative Functional MRI is parent organization of: Myrna is parent organization of: CAWorks is parent organization of: Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data is parent organization of: Longitudinal MS Lesion Imaging Archive is parent organization of: Image Synthesis Tools is parent organization of: Atlases of amygdala and hippocampus for pediatric populations is parent organization of: HISAT2 is parent organization of: neurodata is parent organization of: Johns Hopkins University Integrated Imaging Center Core Facility is parent organization of: Center for Computational Biology at JHU is parent organization of: TopHat is parent organization of: PyRosetta is parent organization of: Ecosystem for Multi-modal Brain-behavior Experimentation and Research is parent organization of: Brain Observatory Storage Service and Database (BossDB) is parent organization of: Johns Hopkins University School of Medicine Genetic Resources Core Facility |
nlx_97251, , Wikidata: Q193727, GRID: grid.21107.35, ISNI: 0000 0001 2171 931, Crossref Funder ID: 100007880 | https://ror.org/00za53h95 | SCR_010247 | 2026-08-01 12:04:06 | 12 | ||||||||
|
VassarStats Resource Report Resource Website 500+ mentions |
VassarStats (RRID:SCR_010263) | software resource | Tools for performing statistical computation including: Clinical Research Calculators Probabilities Distributions Frequency Data Proportions Ordinal Data Correlation & Regression t-Tests & Procedures ANOVA ANCOVA | has parent organization: Vassar College; New York; USA | nlx_156916 | SCR_010263 | VassarStats: Website for Statistical Computation | 2026-08-01 12:04:06 | 965 | ||||||||||
|
TrueSight Resource Report Resource Website 1+ mentions |
TrueSight (RRID:SCR_009835) | TrueSight | software resource | Self-training Algorithm for Splice Junction Detection using RNA-seq. | is listed by: OMICtools | OMICS_01258 | SCR_009835 | 2026-08-01 12:03:46 | 2 | ||||||||||
|
Royal College of Surgeons in Ireland; Dublin; Ireland Resource Report Resource Website |
Royal College of Surgeons in Ireland; Dublin; Ireland (RRID:SCR_009786) | RCSI | university | Private university responsible for the medical speciality of surgery throughout Ireland. |
is related to: Biomedical Diagnostics Institute is parent organization of: Dublin Brain Bank is parent organization of: EPIGEN |
ISNI:0000 0004 0488 7120, grid.4912.e, nlx_143526, Wikidata:Q1124228 | https://ror.org/01hxy9878 | SCR_009786 | Royal College of Surgeons in Ireland | 2026-08-01 12:03:46 | 0 | ||||||||
|
Swiss Commission for Technology and Innovation Resource Report Resource Website 1+ mentions |
Swiss Commission for Technology and Innovation (RRID:SCR_010084) | CTI | government granting agency | SCR_010084 | Commission for Technology and Innovation CTI, Commission for Technology and Innovation, Swiss Commission for Technology Innovation, Swiss Commission for Technology and Innovation CTI | 2026-08-01 12:04:05 | 1 | ||||||||||||
|
Computational Biology and Functional Genomics Laboratory at Harvard Resource Report Resource Website 100+ mentions |
Computational Biology and Functional Genomics Laboratory at Harvard (RRID:SCR_010240) | software resource | A computational biology laboratory that builds and redistributes genetic software tools. |
has parent organization: Harvard University; Cambridge; United States is parent organization of: GeneSigDB |
nlx_156871 | SCR_010240 | Quackenbush Lab | 2026-08-01 12:04:06 | 221 | ||||||||||
|
ABMapper Resource Report Resource Website 1+ mentions |
ABMapper (RRID:SCR_010242) | ABMapper | software resource | A portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping. The core module was written in C++ and wrapped in PERL scripts. | is listed by: OMICtools | OMICS_01238 | SCR_010242 | ABMapper: A suffix-array based spliced alignment tool | 2026-08-01 12:03:47 | 1 | |||||||||
|
Ohio Northern University; Ohio; USA Resource Report Resource Website |
Ohio Northern University; Ohio; USA (RRID:SCR_000362) | ONU | university | A public university in Ohio with land, sea and space grants that offers degree programs and research at the undergraduate and graduate level. | land, sea, space, grant, ohio, public | is parent organization of: Ohio Northern University College of Pharmacy | Wikidata:Q1683585, grid.261323.7, nlx_143792, ISNI:0000 0001 2187 1348 | https://ror.org/052963a64 | SCR_000362 | 2026-08-01 12:01:18 | 0 | ||||||||
|
riboPicker Resource Report Resource Website 1+ mentions |
riboPicker (RRID:SCR_000360) | software resource | Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22155869 | Free, Available for download, Freely available | OMICS_02618, biotools:ribopicker | https://bio.tools/ribopicker | SCR_000360 | 2026-08-01 12:01:15 | 2 | |||||||
|
ARACHNE Resource Report Resource Website 1+ mentions |
ARACHNE (RRID:SCR_000351) | ARACHNE | software resource | A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads. | genome, sequencing, analysis, sanger, chemistry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:11779843 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01812, biotools:arachne | https://bio.tools/arachne | SCR_000351 | ARACHNE: a whole-genome shotgun assembler, ARACHNE (Unsupported) | 2026-08-01 12:01:11 | 3 | |||||
|
ParseCNV Resource Report Resource Website 1+ mentions |
ParseCNV (RRID:SCR_000355) | software resource | Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23293001 | Free, Available for download, Freely available | OMICS_02566 | SCR_000355 | 2026-08-01 12:01:12 | 1 | ||||||||
|
Kinannote Resource Report Resource Website 1+ mentions |
Kinannote (RRID:SCR_000352) | software resource | Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23904509 | Free, Available for download, Freely available | OMICS_05965 | SCR_000352 | 2026-08-01 12:01:18 | 2 | ||||||||
|
HudsonAlpha Genomics Services Lab Resource Report Resource Website |
HudsonAlpha Genomics Services Lab (RRID:SCR_000353) | HudsonAlpha Genomics Services Lab | service resource | A lab that offers genetic research tools such as RNA sequencing and a variety of arrays. | genome, sequencing, assembly, rna, microarray, exome | is listed by: ScienceExchange | THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_221 | SCR_000353 | HudsonAlpha Institute for Biotechnology Genomics Services Lab, Genomics Services Lab | 2026-08-01 12:01:15 | 0 | |||||||
|
Jnomics Resource Report Resource Website |
Jnomics (RRID:SCR_000348) | software resource | A collection of cloud-scale DNA sequence analysis tools. | mapreduce |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_04074 | SCR_000348 | 2026-08-01 12:01:11 | 0 | |||||||||
|
ABrowse Resource Report Resource Website 1+ mentions |
ABrowse (RRID:SCR_000345) | software resource | A genome browser framework which gives an open browsing experience, open data access, collaborative work support, and a framework to import annotations. Multiple data access approaches are supported for external platforms to retrieve data from ABrowse. This resource also contains an online user-space in which users can create, store and share comments, annotations and landmarks. | genome browser, collaborative work, open data access, collaborative work support, framework, import annotation |
is listed by: OMICtools is related to: Galaxy |
PMID:22222089 | Free, Available for download, Freely available | OMICS_00899 | SCR_000345 | 2026-08-01 12:01:11 | 4 | ||||||||
|
GPViz Resource Report Resource Website |
GPViz (RRID:SCR_000346) | GPViz | software resource | A versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants. | gene, visualization, genomic, variant, bioinformatics, java | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_00915 | SCR_000346 | 2026-08-01 12:01:17 | 0 |
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