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https://nrdg.github.io/fracridge

Software tool as regularization technique that penalizes L2-norm of coefficients in linear regression. Available in two programming languages MATLAB and Python.

Proper citation: fracridge (RRID:SCR_019045) Copy   

•   Source: SciCrunch Registry

https://openwetware.org/wiki/RAVE

Open source software tool for reproducible analysis and visualization of intracranial EEG data. Used for analysis of intracranial electroencephalogram data, including data collected using strips and grids (electrocorticography, ECoG) and depth electrodes (stereotactic EEG).

Proper citation: RAVE (RRID:SCR_019040) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/

Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR.

Proper citation: PROCHECK (RRID:SCR_019043) 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

http://www.conplot.org/

Web application for visualisation of information derived from residue contact predictions in combination with other sources of information, such as secondary structure predictions, transmembrane helical topology, sequence conservation.Provides interactive interface for researchers in field of protein bioinformatics that are interested in analysing data on given protein.

Proper citation: ConPlot (RRID:SCR_019216) Copy   

•   Source: SciCrunch Registry

http://markummitchell.github.io/engauge-digitizer/

Software tool accepts image files (like PNG, JPEG and TIFF) containing graphs, and recovers the data points from those graphs. Used to convert graphs to data points. Imports image file and then digitizes it by placing points along axes and curves.

Proper citation: Engauge Digitizer (RRID:SCR_019056) Copy   

•   Source: SciCrunch Registry

https://github.com/bgcarlisle/TRNscreener

Software tool as R script to provide function that takes two arguments: path to folder of plain text files named by their DOI, and output filename. For each file in folder, it searches for trial identifiers based on regex matching and writes CSV that contains all trial registration numbers and in case of ClinicalTrials.gov entries, whether they correspond to registry entry on ClinicalTrials.gov.

Proper citation: Trial Registration Number screener (RRID:SCR_019211) Copy   

•   Source: SciCrunch Registry

http://www.cuemol.org/en/

Software tool for macromolecular structure visualization. Molecular visualization framework to visualize crystallographic models of macromolecules. Used to visualize and create publication quality images of macromolecular structures with user friendly interfaces.

Proper citation: CueMol (RRID:SCR_019052) Copy   

•   Source: SciCrunch Registry

http://www.biosoft.com/w/calcusyn.htm

Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools.

Proper citation: CalcuSyn (RRID:SCR_020251) Copy   

•   Source: SciCrunch Registry

https://thesugarscience.org

Interactive digital platform helping scientists who study type 1 diabetes connect, collaborate, and gain funding for their best ideas. All volunteer team has received much positive support from the global population of scientists studying type 1 diabetes, as well as from Beyond Type 1, JDRF, and IPITA. Provides curated conversations, events and technology to scientific T1D focused audience. Non profit entity funded by donations and sponsorships with industry and academic partners to provide unique collaborative benefits and programs to researchers in the T1D academic research community.

Proper citation: thesugarscience (RRID:SCR_020250) Copy   

•   Source: SciCrunch Registry

https://github.com/Griffan/FASTQuick

Software tool for rapid and comprehensive quality assessment of raw sequence reads. It generates comprehensive list of QC statistics, including ancestry and contamination estimation.

Proper citation: FASTQuick (RRID:SCR_019269) Copy   

•   Source: SciCrunch Registry

https://chanzuckerberg.com/science/programs-resources/single-cell-biology/cellxgene/

Software tool as interactive explorer for single cell transcriptomics datasets. Used to explore and visualize high dimensional single cell datasets in interactive way. Can visualize gene expression at level of entire dataset or particular subset of cells to help identify cell types, which can in turn help identify diseases. Enables plotting gene expression level against another gene to compare how these different genes are expressed across dataset. Open source cell visualization tool integrates with tools like SciPy and Jupyter.

Proper citation: cellxgene (RRID:SCR_021059) Copy   

•   Source: SciCrunch Registry

https://github.com/mjin1812/SMART

Software tool that extends WholeBrain framework in R for segmenting and registering experimental images to Allen Mouse Common Coordinate Framework (CCF). Streamlines processing of large volumetric LSFM datasets and solves issues with non-uniform morphing across anterior-posterior axis with interactive “choice game.” Accounts for duplicate cell counts in adjacent z images and presents new ways to easily parse apart and interactively visualize final mapped datasets.

Proper citation: Semi-Manual Alignment to Reference Templates (RRID:SCR_019265) Copy   

•   Source: SciCrunch Registry

https://ebrains.eu/

Research infrastructure for the EU Human Brain Project. Provides digital tools and services which can be used to address challenges in brain research and brain inspired technology development. Digital research infrastructure, created by EU-funded Human Brain Project, that gathers extensive range of data and tools for brain-related research. EBRAINS will capitalize on the work performed by the Human Brain Project teams in digital neuroscience, brain medicine, and brain-inspired technology.You can share your neuroscience data, models and software.

Proper citation: EBRAINS (RRID:SCR_019260) Copy   

•   Source: SciCrunch Registry

http://eidors3d.sourceforge.net

Free software algorithms for forward and inverse modelling for Electrical Impedance Tomography (EIT) and Diffusion based Optical Tomography, in medical and industrial settings, and to share data and promote collaboration between groups working these fields.

Proper citation: EIDORS:Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software (RRID:SCR_019262) Copy   

•   Source: SciCrunch Registry

https://www.bio-rad.com/en-us/product/ze5-cell-analyzer?ID=OC62Q015

BioRad ZE5 was formerly known as the Propel Labs YETI Cytometer with configurations to meet broad range of experimental complexities and throughput needs. Accessible for novice flow cytometry users yet flexible enough for most experienced flow cytometry professionals.

Proper citation: Bio-Rad: ZE5 Cell Analyzer (RRID:SCR_019712) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/synergyfinder/

Software R package as efficient implementations for all popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of synergy scores as either two dimensional or three dimensional interaction surface over dose matrix. Used to calculate and visualize synergy scores for drug combinations.

Proper citation: SynergyFinder (RRID:SCR_019318) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/fgsea/

Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.

Proper citation: fgsea (RRID:SCR_020938) Copy   

•   Source: SciCrunch Registry

https://www.cmiss.org/cmgui

Standalone application for 3D visualisation and manipulation of mathematical field models. Cmgui is part of Continuum Mechanics, Imaging, Signal processing, System identification mathematical modelling environment. Generic open source modelling and visualisation package used to enable researchers to visualise biomedical images alongside dynamic geometry fields from computer models of cells, tissues and organs.

Proper citation: CMGUI (RRID:SCR_019271) Copy   

•   Source: SciCrunch Registry

https://hugeamp.org

Portal enables browsing, searching, and analysis of human genetic information linked to common metabolic diseases and traits, while protecting integrity and confidentiality of underlying data. Aggregates and analyzes genetic association results, epigenomic annotations, and results of computational prediction methods to provide data, visualizations, and tools in open access portal.

Proper citation: Common Metabolic Diseases Knowledge Portal (RRID:SCR_020937) Copy   

•   Source: SciCrunch Registry