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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Maize Gross Anatomy Ontology Resource Report Resource Website |
Maize Gross Anatomy Ontology (RRID:SCR_010353) | ZEA | ontology, data or information resource, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available. | obo | is listed by: BioPortal | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157462 | http://www.maizemap.org/ | SCR_010353 | 2026-08-08 11:59:28 | 0 | |||||||
|
Major Histocompatibility Complex Ontology Resource Report Resource Website |
Major Histocompatibility Complex Ontology (RRID:SCR_010354) | MHC | ontology, data or information resource, controlled vocabulary | Ontology that contains terms necessary for describing and categorizing concepts related to Major Histocompatibility Complex, in general, for a number of model species, and also for humans. | owl | is listed by: BioPortal | nlx_157463 | SCR_010354 | MaHCO, MaHCO - An MHC Ontology | 2026-08-08 11:59:30 | 0 | ||||||||
|
Microbial Culture Collection Vocabulary Resource Report Resource Website |
Microbial Culture Collection Vocabulary (RRID:SCR_010361) | MCCV | ontology, data or information resource, controlled vocabulary | Structured controlled vocabulary for describing meta information of microbial calture collection maintained in biological research centers | owl | is listed by: BioPortal | nlx_157478 | SCR_010361 | 2026-08-08 11:59:28 | 0 | |||||||||
|
Minimal Information about any Sequence Ontology Resource Report Resource Website |
Minimal Information about any Sequence Ontology (RRID:SCR_010364) | MIXS | ontology, data or information resource, controlled vocabulary | Ontology providing an RDF representation of the MIxS (Minimal Information about any Sequence) family of checklists. | owl | is listed by: BioPortal | nlx_157482 | SCR_010364 | 2026-08-08 11:59:20 | 0 | |||||||||
|
NIF Dysfunction Ontlogy Resource Report Resource Website |
NIF Dysfunction Ontlogy (RRID:SCR_010365) | NIFDYS | ontology, data or information resource, controlled vocabulary | Ontology that contains the former BIRNLex-Disease, version 1.3.2. -- The BIRN Project lexicon provided entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. It was built using the organizational framework provided by the foundational Basic Formal Ontology (BFO). It used an abstract biomedical layer on top of that - OBO-UBO which was constructed as a proposal to the OBO Foundry. This was meant to support creating a sharable view of core biomedical objects such as biomaterial_entity, and organismal_entity that all biomedical ontologies are likely to need and want to use with the same intended meaning. The BIRNLex biomaterial entities have already been factored to separately maintained ontology - BIRNLexBiomaterialEntity.owl which this BIRNLex-Main.owl file imports. The Ontology of Biomedical Investigation (OBI) is also imported and forms the foundation for the formal description of all experiment-related artifacts. The BIRNLex will serve as the basis for construction of a formal ontology for the multiscale investigation of neurological disease. | owl |
is listed by: BioPortal has parent organization: Neuroscience Information Framework |
nlx_157493 | SCR_010365 | Neuroscience Information Framework (NIF) Dysfunction Ontlogy, Neuroscience Information Framework Dysfunction Ontlogy | 2026-08-08 11:59:28 | 0 | ||||||||
|
Skylign Resource Report Resource Website 10+ mentions |
Skylign (RRID:SCR_001176) | Skylign | production service resource, software resource, data analysis service, analysis service resource, service resource | A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. | sequence alignment, profile, logo, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Janelia Research |
PMID:24410852 | Creative Commons Attribution License, v3 Unported | biotools:skylign, OMICS_02182 | https://bio.tools/skylign | SCR_001176 | Skylign - Interactive logos for alignments and profile HMMs | 2026-08-08 11:57:23 | 13 | |||||
|
yaqcaffy Resource Report Resource Website 1+ mentions |
yaqcaffy (RRID:SCR_001295) | yaqcaffy | software resource | Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets. | microarray, one channel, quality control, report writing, affymetrix, gene expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | BioTools:yaqcaffy, biotools:yaqcaffy, OMICS_02040 | http://www.bioconductor.org/packages/release/bioc/html/yaqcaffy.html | SCR_001295 | yaqcaffy - Affymetrix expression data quality control and reproducibility analysis | 2026-08-08 11:57:28 | 3 | ||||||
|
BSSim Resource Report Resource Website 1+ mentions |
BSSim (RRID:SCR_001212) | BSSim | software resource | Software to mimic various methylation level and bisulfite conversion rate in CpG, CHG and CHH context, respectively. It can also simulate genetic variations that are divergent from the reference sequence along with the sequencing error and quality distributions. In the output, both directional/non-directional, various read length, single/paired-end reads and alignment data in the SAM format can be generated. BSSim is a cross-platform BS-seq simulator offers output read datasets not only suitable for Illumina's Solexa, but also for Roche's 454 and Applied Biosystems' SOLiD. | bisulfite sequencing, simulator, next-generation sequencing, python, dna methylation, snp, read quality | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02130 | SCR_001212 | BSSim: Bisulfite sequencing simulator for next-generation sequencing | 2026-08-08 11:57:27 | 1 | |||||||
|
SplicePlot Resource Report Resource Website |
SplicePlot (RRID:SCR_001172) | SplicePlot | software resource | A software tool for visualizing alternative splicing and the effects of splicing quantitative trait loci (sQTLs) from RNA-seq data. It provides a simple command line interface for drawing sashimi plots, hive plots, and structure plots of alternative splicing events from .bam, .gtf, and .vcf files. | visualization, alternative splicing, splicing quantitative trait loci, quantitative trait loci, rna-seq, hive plot, structure plot, sashmi plot, python, linux, mac os, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University School of Medicine; California; USA |
PMID:24363378 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02185, biotools:spliceplot | https://bio.tools/spliceplot | SCR_001172 | SplicePlot: a tool for visualizing alternative splicing | 2026-08-08 11:57:26 | 0 | |||||
|
ChIPsim Resource Report Resource Website 1+ mentions |
ChIPsim (RRID:SCR_001293) | ChIPsim | software resource | Software package providing a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments. | chip-seq, infrastructure, simulation |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or newer | OMICS_02042 | SCR_001293 | ChIPsim - Simulation of ChIP-seq experiments | 2026-08-08 11:57:25 | 1 | |||||||
|
methyAnalysis Resource Report Resource Website 1+ mentions |
methyAnalysis (RRID:SCR_001290) | methyAnalysis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focuses on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data. | dna methylation, microarray, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21159174 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02046 | SCR_001290 | methyAnalysis - DNA methylation data analysis and visualization | 2026-08-08 11:57:25 | 9 | ||||||
|
WiggleTools Resource Report Resource Website 1+ mentions |
WiggleTools (RRID:SCR_001170) | WiggleTools | software toolkit, software library, software resource, software application, data processing software | A multithreaded software library that computes statistics on large numbers of datasets, generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions. | visualization, statistical analysis, parallel processing, genome |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
PMID:24363377 | Apache License, v2 | OMICS_02188 | SCR_001170 | 2026-08-08 11:57:23 | 2 | |||||||
|
les Resource Report Resource Website |
les (RRID:SCR_001291) | les | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package that estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes. | loci of enhanced significance, tiling microarray, tiling, microarray, chip-chip, dna modification, probe, dna methylation, differential expression, microarray, transcription, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:les, OMICS_02045 | https://bioconductor.org/packages/les/, https://bio.tools/les | SCR_001291 | les package: Identifying Differential Effects in Tiling Microarray Data, Loci of Enhanced Significance | 2026-08-08 11:57:39 | 0 | ||||||
|
sim4cc Resource Report Resource Website |
sim4cc (RRID:SCR_001204) | image analysis software, software resource, software application, alignment software, data processing software | Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species. | Cross species spliced alignment, unix, sequence alignment, cdna sequence, genomic sequence, homolog, gene, splice, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johns Hopkins University; Maryland; USA |
NSF CLS20163A; Sloan Research Fellowship ; NLM R01 LM006845 |
PMID:19429899 | Free, Available for download, Freely available | biotools:sim4cc, OMICS_02145 | https://bio.tools/sim4cc | SCR_001204 | 2026-08-08 11:57:24 | 0 | ||||||
|
QualiMap Resource Report Resource Website 10+ mentions |
QualiMap (RRID:SCR_001209) | QualiMap | software resource | Software application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. It examines sequencing alignment data in SAM / BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis. | next-generation sequencing, alignment, linux, macos, windows, quality control, sam, bam, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Principe Felipe Research Centre; Valencia; Spain |
Spanish Ministry of Economy and Competitiveness BIO2009-10799; EU funded program ERA-NET PathoGenoMics BIO2008-05266-E |
PMID:22914218 DOI:10.1093/bioinformatics/bts503 |
Free, Available for download, Freely available | OMICS_02133, biotools:qualimap | https://bio.tools/qualimap | https://sources.debian.org/src/qualimap/ | SCR_001209 | QualiMap - Evaluating next generation sequencing alignment data | 2026-08-08 11:57:39 | 48 | |||
|
Omixon Target Data Analysis Resource Report Resource Website |
Omixon Target Data Analysis (RRID:SCR_001207) | Omixon Target | software toolkit, commercial organization, software resource, software application, data analysis software, data processing software | Software application suite to help clinical labs adopt next generation sequencing for the analysis of diagnostic gene targets. | next-generation sequencing, gene target, windows, linux, mac, gene, diagnostic |
is listed by: OMICtools is parent organization of: Omixon Target HLA Typing |
License required | OMICS_02141 | SCR_001207 | 2026-08-08 11:57:26 | 0 | ||||||||
|
MetaPhyl Resource Report Resource Website |
MetaPhyl (RRID:SCR_001169) | MetaPhyl | software resource | Software implementing a supervised classification method for metagenomic samples that takes advantage of the natural structure of microbial community data encoded by phylogenetic trees. | c++, linux, mac osx, phylogenetic tree, command line, classification, metagenomic |
is listed by: OMICtools has parent organization: University of California at Riverside; California; USA |
PMID:24369151 | Free, Available for download, Freely available | OMICS_02189 | SCR_001169 | 2026-08-08 11:57:26 | 0 | |||||||
|
beadarraySNP Resource Report Resource Website |
beadarraySNP (RRID:SCR_001281) | beadarraySNP | software resource | Software package for importing data from Illumina SNP experiments and performing copy number calculations and reports. | copy number variation, data import, genetic variability, preprocessing, snp, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02056 | http://www.bioconductor.org/packages/devel/bioc/html/beadarraySNP.html | SCR_001281 | beadarraySNP - Normalization and reporting of Illumina SNP bead arrays | 2026-08-08 11:57:25 | 0 | ||||||
|
Baa.pl Resource Report Resource Website |
Baa.pl (RRID:SCR_001197) | Baa.pl | software resource | Software tool to evaluate de novo genome assemblies with RNA transcripts. | genomics, genome assembly, rna transcript, perl | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02154 | https://github.com/josephryan/baa.pl | SCR_001197 | 2026-08-08 11:57:24 | 0 | |||||||
|
VirusHunter Resource Report Resource Website |
VirusHunter (RRID:SCR_001198) | VirusHunter | software resource | A fully automated and modular software package for mining sequence data to identify sequences of microbial origin. The pipeline was optimized for analysis of data generated by the Roche/454 next-generation sequencing platform but can be applied to longer sequences (Sanger sequencing data or assembled contigs) as well. Microbial sequences are identified on the basis of BLAST alignments and the taxonomic classification of the reference sequence(s) to which a read is aligned. Viruses are the focal point of VirusHunter as released, but it can be easily modified to generate parallel outputs for bacterial or parasitic species. To date, VirusHunter has been applied to thousands of specimens, including human, animal and environmental samples, resulting in the detection of many known and novel viruses. | virus, next-generation sequencing, roche, 454, taxonomic classification, alignment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:24167629 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:virushunter, OMICS_02153 | https://bio.tools/virushunter | SCR_001198 | 2026-08-08 11:57:38 | 0 |
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