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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.
Database of free scholary articles. Content from over 50,000 publishers and repositories easy to find, track, and use. A website featuring web-based tools created and maintained by Impactstory, Inc.
Proper citation: Unpaywall (RRID:SCR_016471) Copy
Software tool for microarray analysis designed for biologists . Used for identification of differential expression by providing interactive visualizations.
Proper citation: Transcriptome Analysis Console (RRID:SCR_016519) Copy
https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html
Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.
Proper citation: Entrez (RRID:SCR_016640) Copy
http://www.dhal.com/viewboxindex.htm
Software for cephalometric analysis. Customizable. Allows rendering, viewing and measuring of 3D data from CT scanners. Used in orthodontic departments for analysis of the dental and skeletal relationships of a human skull.
Proper citation: Viewbox4, Cephalometric software (RRID:SCR_016481) Copy
Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics.
Proper citation: PhenoMeNal (RRID:SCR_016605) Copy
https://niaid.github.io/spice/
Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically.
Proper citation: SPICE (RRID:SCR_016603) Copy
System for sharing sleep data. Organization portal that aggregates, harmonizes, and organizes sleep and clinical data from individuals studied as part of cohort studies or clinical trials and provides suite of tools to facilitate data exploration and data visualization. National Heart, Lung, and Blood Institute resource designed to provide big data resources to sleep research community.
Proper citation: National Sleep Research Resource (NSRR) (RRID:SCR_016576) Copy
https://github.com/vetscience/Assemblosis
Software tool as a Common Workflow Language (CWL) based automated bioinformatics workflow to assemble haploid/diploid eukaryote genomes of non-model organisms using PacBio long-reads and Illumina short-reads.
Proper citation: Assemblosis (RRID:SCR_016571) Copy
https://bioinformatics.niaid.nih.gov/netcirchro/
Software interactive tool for visualizing and analyzing network data in the spatial context of the chromosome. Used to discover the role of gene organization in functional regulatory networks. Plugin enables users of Cytoscape to overlay networks onto a circular chromosomal map.
Proper citation: NetCirChro (RRID:SCR_016616) Copy
https://sleepdata.org/datasets/haassa
Portal for sleep-disordered breathing (SDB) in an elderly cohort of Japanese-American men under surveillance for Alzheimer disease (AD) and other dementias. Data to assess relationships between SDB and cognitive performance in late life.
Proper citation: Honolulu-Asia Aging Study of Sleep Apnea (RRID:SCR_016587) Copy
http://metascape.org/gp/index.html#/main/step1
Web service to analyze gene or protein lists. Provides automated meta analysis tools to understand pathways within a group of orthogonal target-discovery studies.
Proper citation: Metascape (RRID:SCR_016620) Copy
https://sleepdata.org/datasets/cfs
Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore.
Proper citation: Cleveland Family Study (RRID:SCR_016585) Copy
https://bioconductor.org/packages/release/bioc/html/Rsubread.html
Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.
Proper citation: Rsubread (RRID:SCR_016945) Copy
Software package to detect and quantify local splicing variations (LSV) from RNA-Seq data. Used to automatically detect and downweight outliers in RNA-Seq datasets with replicates for differential splicing (SD) analysis.
Proper citation: MAJIQ (RRID:SCR_016706) Copy
Portal for sharing spinal cord injury data from basic and clinical research to promote transparency, rigor and reproducibility. Community based repository for spinal cord injury research.
Proper citation: Open Data Commons for Spinal Cord Injury (RRID:SCR_016673) Copy
https://github.com/CPernet/brain_colours
Software tool as a perceptually uniform color maps. Used in scientific literature to reflect data of brain imaging.
Proper citation: Colour maps for brain imaging (RRID:SCR_016715) Copy
https://github.com/xia-lab/MetaboAnalystR
Software R package for comprehensive analysis of metabolomics data. Contains the R functions and libraries underlying MetaboAnalyst web server, including functions for metabolomic data analysis, visualization, and functional interpretation.
Proper citation: MetaboAnalystR (RRID:SCR_016723) Copy
Software package for image acquisition, analysis, display, and archiving. Used to quantify the autoradiography data from Cyclone apparatus from Perkin Elmer.
Proper citation: OptiQuant Software (RRID:SCR_016769) Copy
Web platform for bio image analysis. Used to share knowledge between the different communities, to help biologists to find any tool or workflow available for a particular image analysis problem and to find the adequate image processing wording, to help software and algorithm developers to find missing tools (or components), and to help bioimage analyst to identify and edit workflows.
Proper citation: BISE (RRID:SCR_016774) Copy
https://uk.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image
Matlab based scripts for load, save, make, reslice, view and edit both Neuroimaging Informatics Technology Initiative (NIfTI) and ANALYZE data on any platform.
Proper citation: Tools for NIfTI and ANALYZE image (RRID:SCR_016895) 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.
