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https://integrativeomics.shinyapps.io/pseudofun_app/
Software as database and query tool for homologous pseudogene and coding gene families. Collection of human pseudogenes and gene associations. Supports search, graphical visualization and functional analysis of pseudogenes and coding genes based on PGG families.
Proper citation: PseudoFuN (RRID:SCR_017095) Copy
http://deweylab.biostat.wisc.edu/detonate/
Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences.
Proper citation: DETONATE (RRID:SCR_017035) Copy
https://github.com/epistasislab/hibachi
Software tool that creates data sets with particular characteristics. Method and open source software for simulating complex biological and biomedical data to aid in comparing and evaluating machine learning methods.
Proper citation: Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (RRID:SCR_017140) Copy
http://purl.bioontology.org/ontology/EDDA
Ontology terms useful for machine learning experiments. The terminology appearing in JMLA has been enriched with terms from MeSH and Emtree, the controlled vocabularies for MEDLINE and Embase, respectively. Synonyms include American and British variants and some inverted terms.
Proper citation: EDDA Study Design Terminology (RRID:SCR_010312) Copy
Web tool to predict order and disorder from amino acid sequence. Used to predict of natural disordered regions in proteins.
Proper citation: PONDR (RRID:SCR_023691) Copy
Software tool as robust preprocessing pipeline for functional MRI.Used for preprocessing of diverse fMRI data.
Proper citation: fMRIPrep (RRID:SCR_016216) Copy
https://github.com/lanagarmire/lilikoi
Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction.
Proper citation: lilikoi (RRID:SCR_016361) Copy
Transcription factor target database. Platform consolidating both computationally predicted and experimentally validated binding sites between transfer RNA-derived fragments and target genes or transcripts across multiple organisms.
Proper citation: tTFtarget (RRID:SCR_025631) Copy
https://github.com/slowkoni/rfmix
Software tool for local ancestry and admixture inference. Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference.
Proper citation: RFMix (RRID:SCR_027030) Copy
https://cdemapper.clinicalnlp.org/
Software Common Data Elements (CDEs) mapping tool to bridge the gap between local data elements and National Institutes of Health (NIH) CDEs. Elasticsearch and Large Language Model (LLM)-powered mapping tool designed for biomedical and clinical researchers to efficiently map study variables to the NIH Common Data Elements (CDEs). It integrates essential and advanced services into a user-centered mapping workflow, allowing users to choose different mapping strategies based on their project's needs.Used for enhancing National Institutes of Health common data element use with large language models.
Proper citation: CDEMapper (RRID:SCR_027602) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
