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https://docs.airr-community.org/en/stable/swtools/airr_swtools_standard.html

AIRR Software Guidelines were created by AIRR Software Working Group to promote standards for AIRR software tools and resources in order to enable rigorous and reproducible immune repertoire research at largest scale possible.Established standards for software tools. Authors whose tools comply with this standard will, subject to ratification from AIRR Software WG, be permitted to advertise their tools as being AIRR compliant. Guidelines include compliance checklist, list of compliant tools, and recommended software evaluation data sets.

Proper citation: Adaptive Immune Receptor Repertoire Software Guidelines (RRID:SCR_022595) Copy   

•   Source: SciCrunch Registry

https://docs.airr-community.org/en/stable/datarep/rearrangements.html

Part of AIRR Data Model, defines annotations needed for rearrangements, which are sequences describing rearranged adaptive immune receptor chain (e.g., antibody heavy chain or TCR beta chain). Data for Rearrangement objects are stored as rows in tab delimited file and should be compatible with any TSV reader. Dataset is defined in this context as: TSV file, TSV with companion YAML file containing metadata, or directory containing multiple TSV files and YAML files.

Proper citation: Adaptive Immune Receptor Repertoire Rearrangement Schema (RRID:SCR_022592) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/refseq/about/nonredundantproteins/

Non-redundant RefSeq protein records are currently provided for archaeal and bacterial RefSeq genomes, with exception of selected reference genomes, by NCBI prokaryotic genome annotation pipeline. This scope definition may change in the future to include additional RefSeq sub-kingdoms or other organism groups and some GenBank conceptual translation protein records may provide cross-links to RefSeq non-redundant proteins.

Proper citation: RefSeq non-redundant proteins (RRID:SCR_022748) Copy   

•   Source: SciCrunch Registry

https://orthovenn2.bioinfotoolkits.net/home

Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences.

Proper citation: OrthoVenn2 (RRID:SCR_022504) Copy   

•   Source: SciCrunch Registry

https://www.artec3d.com/portable-3d-scanners/artec-eva

3D scanner for making quick, textured, and accurate 3D models of medium sized objects such as human bust, alloy wheel, or motorcycle exhaust system. Used for capturing objects of almost any kind, including objects with black and shiny surfaces.

Proper citation: Artec 3D: Eva Fast 3D scanner (RRID:SCR_022589) Copy   

•   Source: SciCrunch Registry

https://www.artec3d.com/portable-3d-scanners/artec-spider

3D scanner based on blue light technology. Precision instrument for CAD users and engineers. Used for capturing small objects or intricate details of large industrial objects in high resolution, with accuracy and brilliant color.

Proper citation: Artec 3D: Space Spider (RRID:SCR_022588) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/pavca/

Project related to tracking behavior. Used to identify subgroups of individuals that differentially attribute incentive value to food cue. Includes apparatus for studying Pavlovian conditioned approach behavior. Customized rat PavCA chambers are constructed based on modular devices purchased from Med-Associates. Code used to operate equipment and collect data was written using Med-Associates’ MEDSTATE programming language. This program is then loaded into Med-PC V operating program, also created by Med-Associates.

Proper citation: PavCA project (RRID:SCR_022508) Copy   

•   Source: SciCrunch Registry

https://en.wikipedia.org/wiki/Surgisphere

American healthcare analytics company established in 2008. Originally textbook marketing company, it came under scrutiny in May 2020 after it had provided large datasets of COVID-19 patients which were subsequently found to be extremely unreliable. The questionable data was used in studies published in The Lancet and The New England Journal of Medicine in May 2020. On 15 June 2020, company website was taken offline.

Proper citation: Surgisphere (RRID:SCR_022759) Copy   

•   Source: SciCrunch Registry

http://hollywood.mit.edu/exonscan/

Software framework for modeling sequence motifs based on maximum entropy principle.

Proper citation: ExonScan Web Server (RRID:SCR_022516) Copy   

•   Source: SciCrunch Registry

https://github.com/SGDDNB/ShinyCell

Software R package to create interactive Shiny based web applications to visualise single cell data via visualising cell information and/or gene expression on reduced dimensions e.g. UMAP, visualising coexpression of two genes on reduced dimensions, visualising distribution of continuous cell information e.g. nUMI / module scores using violin plots / box plots, visualising composition of different clusters / groups of cells using proportion plots and visualising expression of multiple genes using bubbleplots / heatmap.Shiny Interactive Web Apps for Single-Cell Data.

Proper citation: ShinyCell (RRID:SCR_022756) Copy   

•   Source: SciCrunch Registry

https://www.licor.com/bio/odyssey-xf/

System includes Odyssey XF Imager and Empiria Studio Software for streamlined image acquisition, organization, and analysis of Western blots. Used for imaging near infrared and enhanced chemiluminescent Western blots, to detect multiple targets on same blot with two channel multiplex fluorescence, and document DNA gels.

Proper citation: LI-COR: Odyssey XF Imaging System (RRID:SCR_022510) Copy   

•   Source: SciCrunch Registry

https://www.antibodysociety.org/the-airr-community/

Research driven group that is organizing and coordinating stakeholders in use of next generation sequencing technologies to study antibody/B-cell and T-cell receptor repertoires. Develops and promotes standards and recommendations for obtaining, analyzing, curating and comparing/sharing AIRR-seq datasets;using and validating tools for analyzing AIRR-seq data;relating AIRR-seq datasets to other “big data” sets, such as microarray, flow cytometric, and MiSeq and single-cell gene-expression data; legal and ethical issues involving use and sharing of AIRR-seq data sets derived from human sources.

Proper citation: AIRR Community (RRID:SCR_022598) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=ComplexUpset

Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries.

Proper citation: ComplexUpset (RRID:SCR_022752) Copy   

•   Source: SciCrunch Registry

https://zdock.umassmed.edu/

Web tool as protein docking server, based on rigid body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers.

Proper citation: ZDOCK Server (RRID:SCR_022518) Copy   

•   Source: SciCrunch Registry

https://github.com/Gaius-Augustus/learnMSA

Software tool as multiple sequence alignment formulated as statistical machine learning problem, where optimal profile hidden Markov model for potentially very large family of protein sequences is searched and alignment is decoded.

Proper citation: learnMSA (RRID:SCR_022572) Copy   

•   Source: SciCrunch Registry

https://github.com/FunctionLab/sei-framework

Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types.

Proper citation: sei (RRID:SCR_022571) Copy   

•   Source: SciCrunch Registry

https://github.com/djamesbarker/pMAT

Open source software suite for analysis of fiber photometry data.

Proper citation: pMAT (RRID:SCR_022570) Copy   

•   Source: SciCrunch Registry

https://github.com/JinmiaoChenLab/Rphenograph

Software R tool as simple R implementation of PhenoGraph algorithm, which is clustering method designed for high dimensional single cell data analysis.

Proper citation: Rphenograph (RRID:SCR_022603) Copy   

•   Source: SciCrunch Registry

https://www.ibm.com/products/structural-equation-modeling-sem

Structural equation modeling software helping support your research and theories by extending standard multivariate analysis methods, including regression, factor analysis, correlation and analysis of variance.

Proper citation: IBM SPSS Amos (RRID:SCR_022686) Copy   

•   Source: SciCrunch Registry

https://quality-preclinical-data.eu/about-eqipd/eqipd-quality-system/

Preclinical research quality system that can be applied in public and private sectors to ensure that early drug development research proceeds along structured lines. Used for ensuring generation of reliable preclinical data. Proposes guidance on expectations for quality related measures, defines criteria for adequate processes like performance standards, and provides examples of how such measures can be developed and implemented. EQIPD certification was established by EQIPD consortium and is now managed by its legacy organisation GoEQIPD.

Proper citation: Enhancing Quality In Preclinical Data Quality System (RRID:SCR_022729) Copy   

•   Source: SciCrunch Registry