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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
https://vanvalen.github.io/about/
Software for segmenting individual cells in microscopy images using deep learning. Cell segmentation software.
Proper citation: DeepCell (RRID:SCR_022197) Copy
http://mummer.sourceforge.net/
Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.
Proper citation: MUMmer (RRID:SCR_018171) Copy
Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data.
Proper citation: LRPath (RRID:SCR_018572) Copy
https://github.com/kilicogluh/limitation-recognizer
Software tool to recognize self acknowledged limitation sentences in biomedical articles. Automatic recognition of self acknowledged limitations in clinical research literature to support efforts in improving research transparency.
Proper citation: Limitation-Recognizer (RRID:SCR_018747) Copy
http://scratch.proteomics.ics.uci.edu/
Web tool as sequence-based, alignment-free and pathogen-independent predictor of protein antigenicity.Predicts likelihood that protein is protective antigen. Integrated in SCRATCH suite of predictors.
Proper citation: ANTIGENpro (RRID:SCR_018779) 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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