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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://www.zeiss.com/microscopy/en/products/light-microscopes/widefield-microscopes/axio-imager-2-for-life-science-research.html

Axio Imager 2 resolves samples from tissue sections in pathology to brain specimens in neuroscience to multi dyed FISH specimens. Works with ZEN imaging software.

Proper citation: Zeiss: Axio Imager 2 (RRID:SCR_018876) 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

http://www.cgga.org.cn/

Web application for data storage and analysis to explore brain tumors datasets from Chinese cohorts. Data portal for storage and interactive exploration of multi-dimensional functional genomic data that includes primary and recurrent glioma samples from Chinese cohorts. Allows users to browse DNA mutation profile, mRNA/microRNA expression profile and methylation profile, and to do correlation and survival analysis in specific glioma subtype.

Proper citation: Chinese Glioma Genome Atlas (RRID:SCR_018802) Copy   

•   Source: SciCrunch Registry

http://faculty.ucr.edu/~mmaduro/random.htm

Web application to generate random DNA sequences.

Proper citation: Random DNA Sequence Generator (RRID:SCR_018768) Copy   

•   Source: SciCrunch Registry

https://github.com/davidebolo1993/TRiCoLOR

Command line application for tandem repeats profiling from error prone long read sequencing data. Works on data from Oxford Nanopore Technologies and Pacific Biosciences sequencers. Used on whole genome alignments.

Proper citation: TRiCoLOR (RRID:SCR_018801) Copy   

•   Source: SciCrunch Registry

https://neurophysics.ucsd.edu/Manuals/Master%208/Master%208%20Eight%20Channel%20Programmable%20Pulse%20Generator.pdf

Pulse generator that can hold 8 different pre-programmed paradigms all of which can use up to all 8 channels.

Proper citation: A.M.P.I.: Master 8 stimulator (RRID:SCR_018889) Copy   

•   Source: SciCrunch Registry

https://beikolab.cs.dal.ca/software/STAMP

Open source software package for analyzing taxonomic or metabolic profiles that promotes best practices in choosing appropriate statistical techniques and reporting results. Graphical software package that provides statistical hypothesis tests and exploratory plots for analyzing taxonomic and functional profiles. Supports tests for comparing pairs of samples or samples organized into two or more treatment groups.

Proper citation: STAMP (RRID:SCR_018887) 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

https://www.coleparmer.in/i/masterflex-l-s-variable-speed-digital-drive-with-remote-i-o-6-to-600-rpm-90-to-260-vac/0752810

Peristaltic pump with flow rate 0.06 to 3400 mL/min, three digit LED display, reversible motor, LED indicators to confirm motor direction and speed range from 6 to 600 rpm.

Proper citation: Cole-Parmer: Masterflex L/S Variable Speed Digital Drive with Remote I/O peristaltic pump (RRID:SCR_019028) 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://ihg.gsf.de/ihg/mitoprot.html

Web server for prediction of mitochondrial targeting sequences.

Proper citation: Mitoprot (RRID:SCR_019023) Copy   

•   Source: SciCrunch Registry

http://genometools.org/

Software tool for de novo detection of full length LTR retrotransposons in large sequence sets. Delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs.

Proper citation: LTRharvest (RRID:SCR_018970) Copy   

•   Source: SciCrunch Registry

https://zlab.bio/guide-design-resources

Laboratory portal about research including new approaches for precision gene editing, delivery of molecular and genetic cargo, discovery of novel programmable systems, and engineering of immune system to develop next generation of therapeutics. Provides collection of tools for guide design.CRISPR.MIT.EDU of Guide Design Tools is no longer available, documented on August 28,2020.

Proper citation: Guide Design Resources (RRID:SCR_018982) Copy   

•   Source: SciCrunch Registry

https://www.bio-rad.com/en-in/product/chemidoc-mp-imaging-system?ID=NINJ8ZE8Z

Instrument for imaging and analyzing gels and western blots by Bio Rad. Designed to address multiplex fluorescent western blotting, chemiluminescence detection, general gel documentation applications, and stain-free technology imaging needs.

Proper citation: Bio-Rad: ChemiDoc MP Imaging System (RRID:SCR_019037) Copy   

•   Source: SciCrunch Registry

https://idseq.net/

Open source cloud based pipeline and analysis service for metagenomic pathogen detection and monitoring. Hypothesis free global software platform that helps scientists identify pathogens in metagenomic sequencing data. IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes assembly based alignment pipeline which results in assignment of reads and contigs to taxonomic categories.

Proper citation: IDseq (RRID:SCR_019038) 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.agilent.com/en/product/software-informatics/mass-spectrometry-software/data-analysis/qualitative-analysis

Mass spectrometry screening software for confirmation of target or suspect compounds, and for identification of unknown analytes. Advanced data mining and processing options let find all detectable compounds and confirm targets or identify unknowns. Results can be displayed using data reporting with either preconfigured reports that simplify basic analyses, or completely customized PDF reports.

Proper citation: Agilent MassHunter Qualitative Analysis (RRID:SCR_019081) Copy   

•   Source: SciCrunch Registry