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https://github.com/neurostuff/NiMARE
Software Python package for coordinate and image based meta analysis of neuroimaging data.
Proper citation: NiMARE (RRID:SCR_017398) Copy
https://www.iconplc.com/innovation/nonmem/
Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions.
Proper citation: NONMEM (RRID:SCR_016986) Copy
https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns.
Proper citation: ComplexHeatmap (RRID:SCR_017270) Copy
Software tool for statistics and data visualization by Red Rock Software, Inc. Provides unparalleled chart selection, data analysis and graph customization capabilities.
Proper citation: Deltagraph (RRID:SCR_018084) Copy
Platform for individuals who want to make their own data available for research. Used by people to join network with others who wish to contribute to vital research in partnership with and alongside leading scientists. Personal tool for saving and displaying medical information.
Proper citation: Hugo Data (RRID:SCR_022763) Copy
https://github.com/linnarsson-lab/loom-viewer
Software tool for sharing, browsing and visualizing single-cell data stored in the Loom file format.
Proper citation: loom-viewer (RRID:SCR_016683) Copy
Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.
Proper citation: MRIcron (RRID:SCR_002403) Copy
HTAN is National Cancer Institute funded Cancer Moonshot initiative to construct 3-dimensional atlases of dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease.Provides three dimensional atlases of cancer transitions for diverse set of tumor types. Efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at single point in time. Data portal for Human Tumor Atlas Network. Data available on HTAN Portal is open access. Certain data types with potential for re-identification are available in restricted access through dbGAP.
Proper citation: Human Tumor Atlas Network (RRID:SCR_023364) Copy
Integrated healthcare biobank that operates under certified conditions and strict SOPs. Enables biomedical and translational researchers to perform their analyses using high quality biospecimens and data to generate reliable and reproducible research data. Core offers modular biobanking portfolio that can cover workflow from blood collection to storage, including all pre-analytical steps and their documentation. Offers spectrum of additional services ranging from DNA/RNA extraction and virtual microscopy to entire management of sample and data flow for national and international research consortia. Provides secure conventional and automated storage of samples at various temperatures as well as secure data management.
Proper citation: Charite University and Berlin Institute for Health Research Central Biobank Core Facility (RRID:SCR_023495) 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
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://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
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
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
https://sourceforge.net/p/iris-scanning/calliope
Software package for image processing for MATLAB. Used for processing of calcium imaging data.
Proper citation: Calliope calcium imaging processing package (RRID:SCR_021213) Copy
https://cumulus.readthedocs.io/en/stable
Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.
Proper citation: Cumulus (RRID:SCR_021644) 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
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