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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.
Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid.
Proper citation: MOON (RRID:SCR_018005) Copy
Probabilistic programming language for specifying statistical models. Defines log probability function over parameters conditioned on specified data and constants. Platform for statistical modeling and high performance statistical computation. Provides full Bayesian inference for posterior expectations including parameter estimation and posterior predictive inference by defining appropriate derived quantities of interest.
Proper citation: Stan (RRID:SCR_018459) Copy
https://github.com/yousra291987/ChiCMaxima
Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling.
Proper citation: ChiCMaxima (RRID:SCR_018178) Copy
http://bioinformatics.fh-hagenberg.at/site/index.php?id=17
Software scoring system to identify peptides out of tandem mass spectrometry data using database of known proteins. Universal identification algorithm optimized for high resolution and high accuracy tandem mass spectra. Software tool as peptide and protein identification algorithm developed by Bioinformatics Research Group University of Applied Sciences Upper Austria in close cooperation with group of Karl Mechtler at IMP Vienna, Austria.
Proper citation: MS Amanda (RRID:SCR_018396) Copy
http://statistika.mfub.bg.ac.rs/interactive-dotplot/
Web-based tool to create customized interactive graphics, including univariate scatterplots, box plots, and violin plots, for comparing values of continuous variable across different study groups, visualization of subgroups or clusters of non-independent data. Web visualization tool for creating dot plots, box plots and violin plots for small sample size data sets.
Proper citation: Interactive Dotplot (RRID:SCR_018329) Copy
Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools.
Proper citation: NeMO Analytics (RRID:SCR_018164) Copy
Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis.
Proper citation: Database of Immune Cell Epigenomes (RRID:SCR_018259) Copy
https://github.com/lmb-embrapa/machado
Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code.
Proper citation: Machado (RRID:SCR_018428) Copy
http://gpcr.biocomp.unibo.it/predgpi/pred.htm
Prediction system for GPI-anchored proteins. Used to predict presence of GPI-anchor and position of omega site. Prediction server based on support vector machine for discrimination of anchoring signal, and on Hidden Markov Model for prediction of most probable omega site. Method for screening whole proteomes.
Proper citation: PredGPI (RRID:SCR_018363) Copy
http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi
Web server for anisotropy of diffraction limit and Bayesian estimation of structure amplitudes by Global Phasing Limited. Server uses DEBYE and STARANISO software to perform anisotropic cut off of merged intensity data, to perform Bayesian estimation of structure amplitudes and to apply anisotropic correction to data.
Proper citation: STARANISO (RRID:SCR_018362) Copy
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
http://www.nitrc.org/projects/reprocontainers/
Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments.
Proper citation: ReproNim/containers (RRID:SCR_018467) Copy
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
http://dambe.bio.uottawa.ca/DAMBE/dambe.aspx
Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers.
Proper citation: DAMBE (RRID:SCR_018528) Copy
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
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
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
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