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http://www.bioconductor.org/packages/release/bioc/html/RMassBank.html

Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Proper citation: RMassBank (RRID:SCR_002797) Copy   

•   Source: SciCrunch Registry

https://github.com/Lcornet/GENERA

Software toolbox to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes.

Proper citation: GENERA (RRID:SCR_023113) Copy   

•   Source: SciCrunch Registry

http://ohnlp.org/index.php/ICEPO

An ontology distributed in OWL format which contains comprehensive terms describing ion channel electrophysiology. Terms from related ontologies, such as Cell Physiology Ontology (CPO), Cardiac Electrophysiology Ontology (CEPO), and Unit Ontology, were integrated into ICEPO.

Proper citation: ICEPO (RRID:SCR_014359) Copy   

•   Source: SciCrunch Registry

https://www.bio-techne.com/resources/instrument-software-download-center/compass-software-simple-western

Simple Western instrument software to analyze assay data and processes results.

Proper citation: Compass for Simple Western (RRID:SCR_022930) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=ggsignif

Software package to indicate if two groups are significantly different. Used to add significance brackets to ggplots.

Proper citation: ggsignif (RRID:SCR_023047) Copy   

•   Source: SciCrunch Registry

https://github.com/Genomon-Project

Software DNA and RNA sequence analysis pipeline.

Proper citation: GenomonPipeline (RRID:SCR_022989) Copy   

•   Source: SciCrunch Registry

https://github.com/nextgenusfs/funannotate

Software package for genome annotation. Built specifically for fungi, but will also work with higher eukaryotes. Used for genome prediction, annotation, and comparison.

Proper citation: funannotate (RRID:SCR_023039) Copy   

•   Source: SciCrunch Registry

https://github.com/open2c/pairtools

Software command line framework to process sequencing data from Hi-C experiment. Used to process pair end sequence alignments.

Proper citation: pairtools (RRID:SCR_023038) Copy   

•   Source: SciCrunch Registry

https://github.com/hartwigmedical/hmftools/blob/master/purple/README.md

Software tool as purity ploidy estimator for whole genome sequenced data. Used for copy number calling and determination of sample purity.

Proper citation: PURPLE (RRID:SCR_022999) Copy   

•   Source: SciCrunch Registry

https://github.com/walaj/svaba

Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements.

Proper citation: SvABA (RRID:SCR_022998) Copy   

•   Source: SciCrunch Registry

https://www.pinnaclet.com/sleepPRO.html

Software tool to reduce scoring time and simplify data analysis. Offers automated power analysis, semi-automated scoring methods, and advanced tabular and graphical analysis for investigating sleep data sets. Custom scoring and analysis are also available. Scoring sessions between two or more users can be compared. All EEG/EMG and video data sets recorded with Pinnacle software, as well as third party EDF files, can be imported.

Proper citation: Sirenia Sleep Pro (RRID:SCR_022918) Copy   

•   Source: SciCrunch Registry

https://www.genoscope.cns.fr/brassicanapus/

Web tool as Brassica napus genome browser.

Proper citation: CNS Genoscope (RRID:SCR_023020) Copy   

•   Source: SciCrunch Registry

https://github.com/c-zhou/yahs

Software command line tool for construction of chromosome scale scaffolds from Hi-C data. Scaffolding tool using Hi-C or Omni-C data. Used to scaffold contig level assemblies into chromosome scale scaffolded assemblies.

Proper citation: YaHS (RRID:SCR_022965) Copy   

•   Source: SciCrunch Registry

http://www.evidenceontology.org

A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2

Proper citation: ECO (RRID:SCR_002477) Copy   

•   Source: SciCrunch Registry

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

Ontology that describes the content of the models used in medical image simulation developed in the context of the Virtual Imaging Platform project (VIP), a french project aiming at sharing medical image simulation resources. This ontology can be used to annotate such models in order to highlight the different entities that are present in the 3D scene to be imaged, i.e. anatomical structures, pathological structures, foreign bodies, contrast agents etc. The model allows also to associate to these entities information about their physical qualities, which are used in the medical image simulation process (to mimick physical phenomena involved in CT, MR, US and PET imaging). This ontology partly relies on the OntoNeuroLOG ontology (ONL-DP ONL-MR-DA), as well as PATO, RadLex, FMA and ChEBI.

Proper citation: Medical image simulation (RRID:SCR_010355) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ONL-MSA

Ontology that is a module of the OntoNeuroLOG ontology that covers the field of mental state assessments, i.e. instruments, instrument variables, assessments, and resulting scores, developed in the context of the NeuroLOG project, a french project aiming at integrating distributed heterogeous resources in neuroimaging. It includes a generic domain core ontology, that provides a general model of such entities and a general taxonomy of behavioural, neurosychological and neuroclinical instruments, that can be easily extended to model any particular kind of instrument. It also includes such extensions for 8 relatively standard instruments, namely: (1) the Beck-depression-inventory-(BDI-II), (2) the Expanded-Disability-Status-Scale, (3) the Controlled-oral-word-association-test, (4) the Free-and-Cued-Selective-Reminding-Test-with-Immediate-Recall-16-item-version-(The-Grober-and-Buschke-test), (5) the Mini-Mental-State, (6) the Stroop-color-and-word-test, (7) the Trail-making-test-(TMT), (8) the Wechsler-Adult-Intelligence-Scale-third-edition, (9) the Clinical-Dementia-Rating-scale, (10) the Category-verbal-fluency, (11) the Rey-Osterrieth-Complex-Figure-Test-(CFT).

Proper citation: Mental State Assessment (RRID:SCR_010357) Copy   

•   Source: SciCrunch Registry

http://www.abbiotec.com/

An Antibody supplier

Proper citation: Abbiotec (RRID:SCR_013596) Copy   

•   Source: SciCrunch Registry

https://www.emkatech.com/product/iox2-software/

Software tool to acquire, analyze, view, and store physiological data generated during preclinical experiment. Has library of application specific analysis modules for real time signal processing.

Proper citation: IOX2 (RRID:SCR_022973) Copy   

•   Source: SciCrunch Registry

https://humantumoratlas.org

HTAN is National Cancer Institute funded Cancer Moonshot initiative to construct 3-dimensional atlases of dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease.Provides three dimensional atlases of cancer transitions for diverse set of tumor types. Efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at single point in time. Data portal for Human Tumor Atlas Network. Data available on HTAN Portal is open access. Certain data types with potential for re-identification are available in restricted access through dbGAP.

Proper citation: Human Tumor Atlas Network (RRID:SCR_023364) Copy   

•   Source: SciCrunch Registry

http://fairbydesign.nl

Software metadata ingestion platform that helps to improve quality of metadata. Station allows users to record meta-data according to minimum information standards thereby ensuring FAIR scientific data management from the start.

Proper citation: FAIR Data Station (RRID:SCR_023239) Copy   

•   Source: SciCrunch Registry