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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
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
https://www.genoscope.cns.fr/brassicanapus/
Web tool as Brassica napus genome browser.
Proper citation: CNS Genoscope (RRID:SCR_023020) Copy
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
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
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
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
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
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
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
http://naturalscenesdataset.org/
Portal for large scale fMRI dataset conducted at ultra high field strength at Center of Magnetic Resonance Research at University of Minnesota. Dataset consists of whole brain, high resolution fMRI measurements of healthy adult subjects while they viewed thousands of color natural scenes over course of scan sessions. While viewing these images, subjects were engaged in continuous recognition task in which they reported whether they had seen each given image at any point in experiment. These data constitute massive benchmark dataset for computational models of visual representation and cognition, and can support wide range of scientific inquiry.
Proper citation: Natural Scenes Dataset (RRID:SCR_023648) Copy
https://www.intelligent-imaging.com/slidebook.php
Digital microscopy software for research microscopy. It comes standard with drivers to control numerous instruments in and around the microscope. When online, data is acquired in a native-3D format over time, color and specimen locations in customizable experiment protocols. Data can be analyzed by a wide variety of tools for image processing including mathematical operations, statistics functions, analysis scripting and import to/export from MATLAB. Additional modules are available for special applications ranging from deconvolution to photomanipulation to multiphoton.
Proper citation: SlideBook (RRID:SCR_014423) Copy
https://cell-innovation.nig.ac.jp/maser/Tools/visualization_top_en.html
One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGffToGe_db for custom genome software loads GFF files of custom genomes to a database for Genome Explorer. It allows the user to browse the results through the GE.
Proper citation: loadGffToGe_db for custom genome (RRID:SCR_015997) Copy
http://github.com/VH-Lab/vhlab-TwoPhoton-matlab
Software VH Lab tools for analysis of calcium imaging data. Allows selection of ROIs and extraction of time series data from raster-scanned, line-scanned, or CCD images, written in Matlab.
Proper citation: vhlab-TwoPhoton-matlab (RRID:SCR_023369) Copy
https://bdcw.org/MetGENE/index.php
Web tool identifies associations between genes and metabolites that are biosynthesized, metabolized, or transported by proteins coded by genes. Gene centric metabolomics information retrieval tool. Knowledge based, gene centric data aggregator that hierarchically retrieves information about genes, their related pathways, reactions,metabolites, and metabolomic studies from standard data repositories under one dashboard to enable ease of access through centralization of relevant information. Information can be contextualized by filtering along species, anatomy tissue and disease or phenotype.
Proper citation: MetGENE (RRID:SCR_023402) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Partec uses FloMax software on most cytometers, which produces FCS 3.0 compliant files. FloMax rescales the fluorescent data on the acquisition display without changing the stored values.
Proper citation: partec flomax (RRID:SCR_014026) Copy
https://github.com/hetio/hetmatpy
Software Python package for matrix storage and operations on hetnets. Enables identifying relevant network connections between set of query nodes.
Proper citation: HetMatPy (RRID:SCR_023409) Copy
Center whose goals include fostering collaboration among basic and clinical investigators, facilitating the use of new technologies in the study of treatment of digestive diseases, and providing education and training for improved treatment and diagnosis.
Proper citation: University of Chicago Digestive Diseases Research Core Center (RRID:SCR_015601) Copy
https://pillow.readthedocs.io/en/stable/
Software Python Imaging Library adds image processing capabilities to your Python interpreter. This library provides extensive file format support, efficient internal representation, and image processing capabilities. Core image library is designed for fast access to data stored in few basic pixel formats. It should provide solid foundation for general image processing tool.
Proper citation: pillow (RRID:SCR_023337) Copy
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