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Software experimental data table management system to make research data accessible and available for reuse with minimal effort on part of data provider. Allows any scientist or data researcher to be able to explore dataset and then extract some or all of data according to their needs. Designed to manage experimental data tables in quick and easy way for users.
Proper citation: ODAM (RRID:SCR_018774) Copy
http://bioinf.wehi.edu.au/software/elda/
Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly.
Proper citation: ELDA (RRID:SCR_018933) Copy
https://github.com/aplbrain/saber
Library of containerized tools and workflow deployment system for enabling processing of large neuroimaging datasets. Provides canonical neuroimaging workflows specified in standard workflow language (CWL), integration with workflow execution engine (Airflow), imaging database (bossDB), and parameter database (Datajoint) to deploy workflows at scale, and tools to automate deployment and optimization of neuroimaging pipelines.
Proper citation: Scalable Analytics for Brain Exploration Research (RRID:SCR_018812) Copy
https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_phd.html
Web tool for secondary structure prediction. Used for network protein sequence analysis.
Proper citation: PHD SECONDARY STRUCTURE (RRID:SCR_018778) Copy
https://github.com/biocatiit/musclex
Software suite as collection of programs intended to assist with analyzing diffraction X-ray images. MuscleX diffraction X-ray image analyzing toolkit. Data reduction software for X-ray fiber diffraction data.
Proper citation: Muscle X (RRID:SCR_018811) Copy
https://github.com/Trinotate/Trinotate.github.io/wiki
Software annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
Proper citation: Trinotate (RRID:SCR_018930) Copy
http://www.genscript.com/psort/psort2.html
Web tool for prediction of protein sorting signals and localization sites in amino acid sequencies. Recommended for animal/yeast sequences. Analyzes input sequence by applying stored rules for various sequence features of known protein sorting signals to report possiblity for input protein to be localized at each candidate site with additional information.
Proper citation: PSORT II (RRID:SCR_018772) Copy
https://github.com/chris-mcginnis-ucsf/DoubletFinder
Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data.
Proper citation: DoubletFinder (RRID:SCR_018771) Copy
http://webapps.embl-hamburg.de/rapido/
Web server for alignment of protein structures in presence of conformational changes. Used for 3D alignment of crystal structures of different protein molecules in presence of conformational change. Can identify structurally equivalent regions also when distant in terms of sequence and separated by other movable domains.
Proper citation: RAPIDO (RRID:SCR_018935) Copy
Web tool where one component is front end Xena Browser and another component is back end Xena Hubs. Web based Xena Browser empowers biologists to explore data across multiple Xena Hubs with variety of visualizations and analyses. Xena Hubs host genomics data from laptops, public servers, behind firewall, or in cloud, and can be public or private. Xena Browser receives data simultaneously from multiple Xena Hubs and integrates them into single coherent visualization within browser. Allows users to explore functional genomic data sets for correlations between genomic and/or phenotypic variables.
Proper citation: UCSC Xena (RRID:SCR_018938) Copy
https://hartleys.github.io/QoRTs/
Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R.
Proper citation: QoRTs (RRID:SCR_018665) Copy
http://smithlabresearch.org/software/preseq/
Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries.
Proper citation: Preseq (RRID:SCR_018664) Copy
Website for study pre-registration. Defines minimum required criteria for pre-registration and allows authors to pre-register their study. It is standardized pre-registration that requires only what is necessary to separate exploratory from confirmatory analyses.
Proper citation: AsPredicted (RRID:SCR_018789) Copy
http://crdd.osdd.net/raghava/algpred/
Web tool for prediction of allergens based on similarity of known epitope with any region of protein. Used for prediction of allergenic proteins and mapping of IgE epitopes.
Proper citation: AlgPred (RRID:SCR_018780) Copy
Functional gene pipeline and repository. Functional gene repository provides collections of genes in interactive platform, while functional gene pipeline offers suite of tools for functional gene amplicon processing and analysis. Together they enable key steps in functional gene based microbial community analysis, from target selection and primer analysis to amplicon processing and ecological discovery.
Proper citation: FunGene (RRID:SCR_018749) Copy
https://nanopore.usegalaxy.eu/
Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance.
Proper citation: NanoGalaxy (RRID:SCR_018912) Copy
https://github.com/HicServices/BadMedicine
Software library and command line tool for generating realistic looking synthetic Electronic Health Records data for testing purposes.
Proper citation: BadMedicine (RRID:SCR_018879) Copy
https://mcguinlu.shinyapps.io/robvis/
Software R package and web app, which facilitates rapid production of publication quality risk of bias assessment figures. Used to produce high quality figures that summarize the risk-of-bias assessments performed as part of systematic review or research synthesis project.
Proper citation: robvis (RRID:SCR_018755) Copy
https://bioconductor.org/packages/scTHI/
Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment.
Proper citation: scTHI (RRID:SCR_018918) Copy
https://www.t2dsystems.eu/t2dsystems
Project to bridge gap between in vitro human islet studies and clinical studies in human subjects. Used to integrate cellular and medical research data, collected by partners, with computational modelling to identify pathophysiological mechanisms and markers of spectrum of biological and cellular processes involved in pancreatic beta cell failure leading to impaired glucose tolerance and T2D.
Proper citation: T2DSystems (RRID:SCR_018913) Copy
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