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http://www.bioontology.org/wiki/index.php/CARO:Main_Page

An ontology developed to facilitate interoperability between existing anatomy ontologies for different species, and to provide a template for building new anatomy ontologies.

Proper citation: Common Anatomy Reference Ontology (RRID:SCR_003296) Copy   

•   Source: SciCrunch Registry

http://www.decode.com/

A biopharmaceutical company applying its discoveries in human genetics to develop drugs and diagnostics for common diseases. They specialize in gene discovery - their population approach and resources have enabled them to isolate key genes contributing to major public health challenges from cardiovascular disease to cancer. The company's genotyping capacity is now one of the highest in the world. They have a large population-based biobank containing whole blood and DNA samples with extensive relevant phenotypic information from around 120.000 Icelanders. In the company's work in more than 50 disease projects, their statistical and informatics departments have established themselves in data processing and analysis. deCODE genetics is widely recognized as a center of excellence in genetic research.

Proper citation: deCODE genetics (RRID:SCR_003334) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CMO

An ontology designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.

Proper citation: Clinical Measurement Ontology (RRID:SCR_003291) Copy   

•   Source: SciCrunch Registry

http://primerseq.sourceforge.net/

Software that designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data. It is particularly advantageous for designing a large number of primers for validating alternative splicing events found in RNA-Seq data. It incorporates RNA-Seq data in the design process to weight exons by their read counts. Essentially, the RNA-Seq data allows primers to be placed using actually expressed transcripts. This could be for a particular cell line or experimental condition, rather than using annotations that incorporate transcripts that are not expressed for the data. Alternatively, you can design primers that are always on constitutive exons. PrimerSeq does not limit the use of gene annotations and can be used for a wide array of species.

Proper citation: PrimerSeq (RRID:SCR_003295) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/OmicCircos.html

An R software application and package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns.

Proper citation: OmicCircos (RRID:SCR_003292) Copy   

•   Source: SciCrunch Registry

https://github.com/rsc-ontologies/rsc-cmo

An ontology that describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy; preparing and separating material for further analysis, such as sample ionization, chromatography, and electrophoresis; and synthesizing materials, such as epitaxy and continuous vapor deposition. It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).

Proper citation: Chemical Methods Ontology (RRID:SCR_003286) Copy   

•   Source: SciCrunch Registry

http://shendurelab.github.io/MIPGEN/

Software for a fast, simple way to generate designs for MIP assays targeting hundreds or thousands of genomic loci in parallel. Packaged with MIPgen are scripts that aid in visualization of MIP designs and processing of MIP sequence reads to SAM files that can then be passed through any standard variant calling pipeline.

Proper citation: MIPgen (RRID:SCR_003325) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/popoolation2/

Software to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PoPoolation2 (RRID:SCR_003284) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/FB-CV

A structured controlled vocabulary used for various aspects of annotation by FlyBase. This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them.

Proper citation: FlyBase Controlled Vocabulary (RRID:SCR_003318) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/FYPO

A formal ontology of phenotypes observed in fission yeast that is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource. Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions.

Proper citation: Fission Yeast Phenotype Ontology (RRID:SCR_003315) Copy   

•   Source: SciCrunch Registry

https://github.com/outbig/DAFGA

A python script package which estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene. It provides gene-specific parameter sets for OTU clustering and taxonomic assignment at desired rank, and it can be implemented into the diversity measurements offered by QIIME or Mothur.

Proper citation: DAFGA (RRID:SCR_003319) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/johanneskoester/snakemake/wiki/

A Python based language and execution environment for make-like workflows. The system supports the use of automatically inferred multiple named wildcards (or variables) in input and output filenames.

Proper citation: Snakemake (RRID:SCR_003475) Copy   

•   Source: SciCrunch Registry

http://knowledgemap.mc.vanderbilt.edu/research/content/phewas-r-package

Software package contains methods for performing Phenome-Wide Association Study.

Proper citation: PheWAS R Package (RRID:SCR_003512) Copy   

•   Source: SciCrunch Registry

https://github.com/BauerLab/ngsane

Software providing a Linux-based High Performance Computing (HPC) enabled framework for high-throughput data analysis that minimizes overhead for set up and processing of new projects yet maintains full flexibility of custom scripting when processing raw sequence data.

Proper citation: NGSANE (RRID:SCR_003478) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/snape-pooled/

Software that computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.

Proper citation: SNAPE-pooled (RRID:SCR_003476) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/bpipe/

Software tool for running and managing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, it is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments.

Proper citation: Bpipe (RRID:SCR_003471) Copy   

•   Source: SciCrunch Registry

http://www.lgm.upmc.fr/parseq/

Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders.

Proper citation: Parseq (RRID:SCR_003464) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/popcomm-ontology/

An ontology that models material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is compliant with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies, such as the Gene Ontology (GO), which covers biological processes, and the Phenotypic Quality Ontology (PATO).

Proper citation: Population and Community Ontology (RRID:SCR_003462) Copy   

•   Source: SciCrunch Registry

http://archive.gramene.org/plant_ontology/ontology_browse.html#eo

A structured controlled vocabulary for the representation of plant environmental conditions.

Proper citation: Plant Environmental Conditions (RRID:SCR_003460) Copy   

•   Source: SciCrunch Registry

http://ctrad-csi.nus.edu.sg/gbsa/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Software for analyzing whole-genome bisulfite sequencing data.

Proper citation: GBSA (RRID:SCR_003413) Copy   

•   Source: SciCrunch Registry