Tools   Select Another Resource Report Type

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://sedfitsedphat.nibib.nih.gov/software/default.aspx

Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.

Proper citation: SEDFIT (RRID:SCR_018365) Copy   

•   Source: SciCrunch Registry

https://github.com/grecolab/TinderMIX

Software tool as framework for dose and time dependent gene expression analysis which aims to identify groups of genes that show dynamic dose response behaviour. Software R package to cluster gene expression by contour plots. Used to analyse toxicogenomics data with multiple dose levels and time points and to identify expression patterns with respect to both variables and to cluster molecular features.

Proper citation: TinderMIX (RRID:SCR_018364) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   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://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

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://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

https://exrna-atlas.org

Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.

Proper citation: exRNA Atlas (RRID:SCR_017221) Copy   

•   Source: SciCrunch Registry

https://www.hsph.harvard.edu/hmac/

Core assists with consultation for microbiome project development, provides validated meta omic analysis of microbial community data, and supports fully collaborative grant funded investigations.

Proper citation: Harvard School of Public Health Microbiome Analysis Core Facility (RRID:SCR_017187) Copy   

•   Source: SciCrunch Registry

https://github.com/csbbcompbio/CSBB-v3.0

Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments.

Proper citation: Computational Suite for Bioinformaticians and Biologists (RRID:SCR_017234) Copy   

•   Source: SciCrunch Registry

https://t1dexchange.org/research/biobank/

Collection of biological samples linked to participant medical data from individuals living with type 1 diabetes. Unifies samples and data from eight different clinical studies related to type 1 diabetes.

Proper citation: T1D Exchange Biobank (RRID:SCR_017195) Copy   

•   Source: SciCrunch Registry

https://github.com/greenhouselab/Veta

Software suite of functions for EMG data visualization and processing. Open source Matlab toolbox for electromyography combined with transcranial magnetic stimulation. MATLAB toolbox for the collection, analysis, and visualization of EMG and TMS.

Proper citation: VETA (RRID:SCR_017201) Copy   

•   Source: SciCrunch Registry

https://github.com/llawas/Rice_HxD_Recovery_Metabolomics

Software tool as source code used in analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice collected during rewatering after exposure to combined drought and heat stress.

Proper citation: Rice_HxD_Recovery_Metabolomics (RRID:SCR_017204) Copy   

•   Source: SciCrunch Registry