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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.
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
http://www.eulerdiagrams.org/eulerAPE/
Software that uses ellipses to automatically draw accurate area-proportional Venn diagrams for 3-set data. It generates an exact diagram for most of the cases, and when it fails, the best diagram obtained through the hill climbing search is displayed, together with the inaccuracy values for each region.
Proper citation: eulerAPE (RRID:SCR_016457) 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
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://cran.r-project.org/web/packages/dplyr/index.html
Software tool for working with data frame like objects, both in memory and out of memory. It is a grammar of data manipulation, providing a consistent set of verbs that help you solve the most common data manipulation challenges: mutate, select, filer, summerise, arrange.
Proper citation: dplyr (RRID:SCR_016708) 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://cran.r-project.org/web/packages/anocva/index.html
Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders.
Proper citation: ANOCVA (RRID:SCR_016719) 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
Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise.
Proper citation: Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS (RRID:SCR_016657) Copy
https://visrsoftware.github.io/
Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses.
Proper citation: VisR (RRID:SCR_016658) Copy
https://software.broadinstitute.org/gatk/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer.
Proper citation: IndelGenotyper (RRID:SCR_016663) Copy
http://www.cbs.dtu.dk/biotools/sequenza/
Software package for copy number estimation from tumor genome sequencing data.Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.
Proper citation: Sequenza (RRID:SCR_016662) Copy
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