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https://github.com/PatternRecognition/OpenBMI

Software package for the development of Brain-Computer Interfaces with advanced pattern recognition algorithms. Used for analyzing brain signals which can be used to acquire, filter, process, classify and visualize brain signals in real time.

Proper citation: OpenBMI (RRID:SCR_016876) Copy   

•   Source: SciCrunch Registry

https://knoweng.org

Part of the NIH Big Data to Knowledge (BD2K) Initiative. One of 11 Centers of Excellence in Big Data Computing. Platform for genomics data analysis where user-supplied data sets will be analyzed in the context of existing knowledge. E-science framework for genomics where biomedical scientists will have access to powerful methods of data mining, network mining, and machine learning to extract knowledge out of genomics data.

Proper citation: KnowEnG (RRID:SCR_016875) Copy   

•   Source: SciCrunch Registry

https://github.com/dpeerlab/phenograph

Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity.

Proper citation: Phenograph (RRID:SCR_016919) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html

Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.

Proper citation: clusterProfiler (RRID:SCR_016884) Copy   

•   Source: SciCrunch Registry

https://kpmp.org

Project to ethically obtain and evaluate human kidney biopsies from participants with Acute Kidney Injury (AKI) or Chronic Kidney Disease (CKD), create a kidney tissue atlas, define disease subgroups, and identify critical cells, pathways, and targets for novel therapies. Used to develop the next generation of software tools to visualize and understand the various components of kidney diseases and to optimize data collection. Multi site collaboration comprised of patients, clinicians, and investigators from across the United States.

Proper citation: Kidney Precision Medicine Project (RRID:SCR_016920) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/data/experiment/html/affydata.html

Software R package for analysis of Affymetrix Data. Contains samples data files of a large size.

Proper citation: affydata (RRID:SCR_016976) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/quicknii/

Section series aligner to volumetric atlases. Software tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems.

Proper citation: QuickNII (RRID:SCR_016854) Copy   

•   Source: SciCrunch Registry

http://www2.heatmapper.ca/

Software tool to create and provide heat maps through a graphical interface. Allows to create an expression, pairwise comparison, image overlay, geomap, and geocoordinate heat maps for different data types and applications. Used to interactively visualize data.

Proper citation: Heatmapper (RRID:SCR_016974) Copy   

•   Source: SciCrunch Registry

https://www.ccpn.ac.uk/

Project provides tools and knowledge to maximize the impact of the biological NMR studies. CCPN software facilitates data analysis and software integration. Project promotes the exchange of knowledge and provides training and best practices for the NMR community and has leading role in the development of NMR data sharing standard and coordination of NMR instrumentation proposals. Includes CCPN Data Model for macromolecular NMR and related areas, CcpNmr suite of programs like Analysis for spectrum visualization, resonance assignment and analysis, ChemBuild to create chemical structure templates in an NMR aware manner, FormatConverter for data exchange with common textual NMR formats and SpecView for swift, format independent peak and spectrum visualization.

Proper citation: Collaborative Computing Project for NMR (RRID:SCR_016983) Copy   

•   Source: SciCrunch Registry

https://www.ccpn.ac.uk/v2-software/software/extras/datamodelfolder

Model to cover data for macromolecular NMR spectroscopy from the initial experimental data to the final validation. Used for the large scale data deposition, data mining and program interoperability. Enables movement from one software package to another without difficulties with data conversion or loss of information. Works with CcpNmr Analysis software for analysis and interactive display, CcpNmr FormatConverter for allowing transfer of data from programs used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment. Used within the CCPN software suite for NMR spectroscopy and at the BioMagResBank for converting existing deposited restraint lists to a standard IUPAC nomenclature.

Proper citation: CCPN Data Model (RRID:SCR_016982) Copy   

•   Source: SciCrunch Registry

https://www.ccpn.ac.uk/v2-software/software/analysis

Software package for interactive NMR spectrum visualization, resonance assignment and data analysis. Graphical elements allow to enter information and to view status of data and library functions manipulate the CCPN data model objects to record the scientific information. Software is cross platform and works on Linux, Mac OSX, Windows and Unix.

Proper citation: CCPN Analysis (RRID:SCR_016984) Copy   

•   Source: SciCrunch Registry

http://pinet-server.org

Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.

Proper citation: piNET (RRID:SCR_018693) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ggtree/

Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses.

Proper citation: ggtree (RRID:SCR_018560) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://usdrn.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry