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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.
https://github.com/OHDSI/CohortMethod
Software R package for performing new user cohort studies in observational database in OMOP Common Data Model.
Proper citation: CohortMethod (RRID:SCR_018511) Copy
http://tools.dice-database.org/GOnet/)
Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.
Proper citation: GOnet (RRID:SCR_018977) Copy
https://github.com/najasplus/hetindel_shinyapp
Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels.
Proper citation: Hetindel (RRID:SCR_018922) Copy
http://www.mrc-cbu.cam.ac.uk/methods-and-resources/toolboxes/license/
Software Matlab toolbox to perform representational similarity analysis for neural data.
Proper citation: Toolbox for Representational Similarity Analysis (RRID:SCR_019029) Copy
https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation
Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer.
Proper citation: CLIP Tool Kit (RRID:SCR_019034) Copy
https://www.openicpsr.org/openicpsr/covid19
Repository for data examining social, behavioral, public health, and economic impact of novel coronavirus global pandemic. Free self publishing option for any researcher who wants to share data related to COVID-19. Deposits should include all data, annotated program code, command files, and documentation necessary to understand data collection and/or replicate research findings.
Proper citation: COVID-19 Data Repository (RRID:SCR_019105) Copy
https://trials.bgcarlisle.com/
Software tool to download and parse information from ClinicalTrials.gov at the time of search to populate the graph of clinical trials. FDA information is updated weekly from Drugs at FDA dataset and FDA postmarketing commitment data set.
Proper citation: Clinical Trials Viewer (RRID:SCR_019230) Copy
Portal for research on urinary stones in adults and children in order to learn more about who forms kidney stones, treatments and prevention. Network comprises of experts including adult and pediatric urologists, adult and pediatric nephrologists, pediatricians, emergency department physicians, clinical trialists, nutritionists, behavioral scientists, and radiologists. Duke Clinical Research Institute is Scientific Data Research Center and with clinical sites including University of Pennsylvania Children Hospital of Philadelfia, University of Texas Southwestern Medical Center, University of Washington, Washington University in St. Louis, work together in planning, executing, and analyzing results from USDRN studies.
Proper citation: Urinary Stone Disease Research Network (RRID:SCR_019059) Copy
http://ced.co.uk/products/sigovin
Software package for sweep based data acquisition and analysis of time based waveform data obtained through CED digital analogue converter by Cambridge Electronic Design System Limited. Used for transient capture, patch and voltage clamp, LTP studies, evoked response and TMS.
Proper citation: Signal (RRID:SCR_017081) Copy
https://immunedb.readthedocs.io/en/latest/
Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features.
Proper citation: ImmuneDB (RRID:SCR_017125) Copy
http://bioconductor.org/packages/CATALYST/
Software R package to provide pipeline for preprocessing of cytometry data, including normalization using bead standards, single cell deconvolution, and bead based compensation.
Proper citation: CATALYST (RRID:SCR_017127) Copy
https://github.com/cancerit/cgpBattenberg
Software tool as installation helper, perl wrapper and R program Battenberg which detects subclonality and copy number in matched NGS data.
Proper citation: cgpBattenberg (RRID:SCR_017092) Copy
Issue
https://biit.cs.ut.ee/clustvis/
Web user interface for visualizing clustering of multivariate data. Web server allows users to upload their own data and create Principal Component Analysis plots and heatmaps.
Proper citation: ClustVis (RRID:SCR_017133) Copy
Core to assist with analyzing and interpreting data produced by genomic technologies.
Proper citation: University of North Carolina Charlotte Bioinformatics Services Division (RRID:SCR_017182) Copy
http://bioconductor.org/packages/gage/
Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies.
Proper citation: GAGE (RRID:SCR_017067) Copy
https://www.cityofhope.org/research/shared-resources/integrative-genomics-and-bioinformatics
Core provides genomic and bioinformatics services to City of Hope Comprehensive Cancer Center (COHCCC) investigators.
Proper citation: City of Hope National Medical Center Integrative Genomics and Bioinformatics Core Facility (RRID:SCR_017188) Copy
https://www.hsph.harvard.edu/hmac/
Core assists with consultation for microbiome project development, provides validated meta omic analysis of microbial community data, and supports fully collaborative grant funded investigations.
Proper citation: Harvard School of Public Health Microbiome Analysis Core Facility (RRID:SCR_017187) Copy
https://t1dexchange.org/research/biobank/
Collection of biological samples linked to participant medical data from individuals living with type 1 diabetes. Unifies samples and data from eight different clinical studies related to type 1 diabetes.
Proper citation: T1D Exchange Biobank (RRID:SCR_017195) Copy
https://github.com/llawas/Rice_HxD_Metabolomics
Source code used in the analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice exposed to combined drought and heat stress.
Proper citation: Source code for analysis of GC-MS data - Rice HxD Project (RRID:SCR_017073) Copy
https://www.plantsci.cam.ac.uk/bioinformatics
Core provides assistance in data analysis to support members of Plant Sciences.
Proper citation: University of Cambridge Department of Plant Sciences Bioinformatics Core Facility (RRID:SCR_017164) Copy
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