Tools   Select Another Resource Report Type

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://aspredicted.org

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   

•   Source: SciCrunch Registry

https://github.com/wangdingkang/DiscreteMorse

Discrete Morse based pipeline for neuron tracing on tracer injection and single neuron data sets. Automatically generates set of trees summarization of given neuron imaging data. Used to extract tree skeletons of individual neurons from volumetric brain image data, and to summarize collections of neurons labelled by tracer injections.

Proper citation: Discrete Morse (RRID:SCR_018662) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/minet/

Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data.

Proper citation: minet (RRID:SCR_018661) Copy   

•   Source: SciCrunch Registry

http://fungene.cme.msu.edu/

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   

•   Source: SciCrunch Registry

https://www.siemens-healthineers.com/en-us/angio/options-and-upgrades/clinical-software-applications/syngo-dynact

Software tool to construct 3D models of soft tissue using CT-like cross sectional imaging.

Proper citation: syngo DynaCT (RRID:SCR_018902) Copy   

•   Source: SciCrunch Registry

http://rats.pub

Web service that conducts comprehensive literature mining to identify roles of genes in addiction. Searches PubMed to find abstracts containing genes of interest and list of curated addiction related keywords.

Proper citation: RatsPub (RRID:SCR_018905) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/abcdrepronim/

Course provides training for reproducible analyses of Adolescent Brain Cognitive Development Study data. Designed to provide comprehensive background to ABCD study while delivering hands on instruction on reproducible ReproNim workflows and outcomes.

Proper citation: ABCD-ReproNim Course (RRID:SCR_018911) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://diabeticfootconsortium.org/

Group of academic institutions committed to studying diabetic foot conditions, such as foot ulcers and wound healing, to develop predictive biomarkers which can be later used to create better treatment plans and improve health and quality of life for people living with diabetes.

Proper citation: Diabetic Foot Consortium (RRID:SCR_018914) Copy   

•   Source: SciCrunch Registry

https://github.com/ylab-hi/ScanITD

Open source software Python tool for detecting internal tandem duplication with variant allele frequency estimation.

Proper citation: ScanITD (RRID:SCR_018886) Copy   

•   Source: SciCrunch Registry

https://rosie.graylab.jhu.edu/docking2

Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community.

Proper citation: ROSIE (RRID:SCR_018764) Copy   

•   Source: SciCrunch Registry