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http://www.cbs.dtu.dk/services/NetMHCpan/
Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs).
Proper citation: NetMHCpan Server (RRID:SCR_018182) Copy
Portal to make cancer related proteomic datasets easily accessible to public. Facilitates multiomic integration in support of precision medicine through interoperability with other resources. Developed to advance our understanding of how proteins help to shape risk, diagnosis, development, progression, and treatment of cancer. One of several repositories within NCI Cancer Research Data Commons which enables researchers to link proteomic data with other data sets (e.g., genomic and imaging data) and to submit, collect, analyze, store, and share data throughout cancer data ecosystem. PDC provides access to highly curated and standardized biospecimen, clinical, and proteomic data, intuitive interface to filter, query, search, visualize and download data and metadata. Provides common data harmonization pipeline to uniformly analyze all PDC data and provides advanced visualization of quantitative information. Cloud based (Amazon Web Services) infrastructure facilitates interoperability with AWS based data analysis tools and platforms natively. Application programming interface (API) provides cloud-agnostic data access and allows third parties to extend functionality beyond PDC. Structured workspace that serves as private user data store and also data submission portal. Distributes controlled access data, such as patient-specific protein fasta sequence databases, with dbGaP authorization and eRA Commons authentication.
Proper citation: Proteomic Data Commons (RRID:SCR_018273) Copy
https://github.com/nci/drishti
Open source scientific visualisation software. Multi platform, volume exploration and presentation software. Used for visualising volumetric data, such as tomography data, electron microscopy data, etc.
Proper citation: Drishti (RRID:SCR_017999) Copy
https://www.volumegraphics.com/de/produkte/vgstudio.html
Software tool for analysis and processing of µCT data, e.g. compiling virtual 3D models of morphological structures in site by Volume Graphics GmbH. Used for visualization of CT data.
Proper citation: VG Studio MAX (RRID:SCR_017997) Copy
Software package for analysis of expression dynamics in single cell RNA seq data. Enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. Estimates RNA velocity in single cell RNA sequencing datasets. RNA velocity estimation in Python or R.
Proper citation: Velocyto (RRID:SCR_018167) Copy
https://github.com/astroML/astroML
Software Python package for machine learning, statistics and data mining. Contains library of statistical and machine learning routines for analyzing astronomical data in Python, loaders for several open astronomical data sets, and examples of analyzing and visualizing astronomical data sets. Repository of common tools and routines used for statistical data analysis in astronomy and astrophysics.
Proper citation: astroML (RRID:SCR_018138) Copy
https://github.com/r3fang/SnapTools
Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets.
Proper citation: SnapTools (RRID:SCR_018097) Copy
Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data.
Proper citation: Global Initiative on Sharing All Influenza Data (RRID:SCR_018251) Copy
Open source software application with data analysis tools and spreadsheet templates used to manage, process and visualize data. LibreOffice Calc is spreadsheet component of LibreOffice software package developed by Document Foundation.
Proper citation: LibreOfficeCalc (RRID:SCR_018013) Copy
https://amp.pharm.mssm.edu/covid19/
Software tool as interface to submit, serve, and analyze COVID19 related gene and drug sets. Collection of gene and drug sets related to COVID-19 research contributed by community.
Proper citation: COVID-19 Crowd Generated Gene and Drug Set Library (RRID:SCR_018252) Copy
Community software Pyton library for astronomy. Collection of software packages written in Python programming language for use in astronomy. Package contains key functionality and common tools needed for performing astronomy and astrophysics with Python. Core of Astropy Project, which aims to enable community to develop ecosystem of Affiliated Packages covering broad range of needs for astronomical research, data processing, and data analysis.
Proper citation: astropy (RRID:SCR_018148) Copy
https://github.com/shanemomara/omaraneurolab/tree/master/NeuroChaT
Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories.
Proper citation: NeuroChaT (RRID:SCR_018020) Copy
Web provides tools for modeling 3D structures of molecules and complexes containing carbohydrates including oligosaccharide conformation modeling and glycoprotein 3D structure modeling. Used to simplify prediction of three dimensional structures of carbohydrates and macromolecular structures involving carbohydrates.
Proper citation: GLYCAM-Web (RRID:SCR_018260) Copy
https://tripod.nih.gov/curvefit/
Large scale dose response curve fitting and curve classification software. Automated curve fitting and classificatoin software. Web deployed software. Algorithm recognizes bell shaped curves, implements standard hill equation, extensible for other models.
Proper citation: NCGC CurveFit (RRID:SCR_018079) Copy
https://github.com/galaxyproteomics/mvpapplication-git.git
Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach.
Proper citation: Multi-omics Visualization Platform (RRID:SCR_018077) Copy
https://CRAN.R-project.org/package=biomod2
Software R package for species distribution modeling, calibration and evaluation, ensemble of models, ensemble forecasting and visualization.
Proper citation: biomod2 (RRID:SCR_018246) Copy
http://sourceforge.net/projects/cnv-webstore
Integrated platform to analyse, store, visualise and interpret CopyNumber Variation data. Analysis is supported for Illumina data, all CNV-reports and raw data can be imported after third-party analysis. Platform to streamline processing and downstream interpretation of microarray data in clinical context. Analysis tools include CNV analysis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases.
Proper citation: CNV webstore (RRID:SCR_018007) Copy
http://statistika.mfub.bg.ac.rs/interactive-linegraph/
Interactive web based tool for creating line graphs for scientific publications. Users can view different summary statistics, examine lines for any individual in data, focus on time points or groups of interest, and view changes between any two time points and conditions.
Proper citation: Interactive Line Graph (RRID:SCR_018334) Copy
https://huygens.science.uva.nl/PlotsOfData/
Web app for visualizing data together with their summaries. Visualizes data and statistics to enable comparison of experimental conditions. Written in R and uses packages including shiny, ggplot2, dplyr, tidyr, readr, magrittr, ggbeeswarm, readxl, DT. Github page of PlotsOfData can be used to trace changes between different versions.
Proper citation: PlotsOfData (RRID:SCR_018333) Copy
https://webs.iiitd.edu.in/raghava/coronavir
Web based platform on COVID-19 to maintain predicted diagnostic, drug and vaccine candidates and computational resources on novel coronavirus SARS-CoV-2 and its resulting disease COVID-19. Provides collected and organized information from literature and other resources from internet, links to appropriate literature . Integrated multi-omics repository dedicated to current genomic, proteomic, diagnostic and therapeutic knowledge about coronaviruses.
Proper citation: CoronaVIR (RRID:SCR_018338) Copy
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