Curator Dashboard

Checklist of minimally required information that we recommend journals adopt, and that could form requirements for submission to public data repository. AIRR sequencing studies apply high throughput sequencing technologies to profile B cell receptors (BCRs) and T cell receptors (TCRs). Standards were developed by AIRR Community Minimal Standards Working Group.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

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.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

Defines schema for MiAIRR data elements, structuring them within schema objects, defining relationship between those objects, and defining file format. Increased interest in immune system's involvement in pathophysiological phenomena coupled with decreased DNA sequencing costs have led to explosion of antibody and T cell receptor sequencing data collectively termed "adaptive immune receptor repertoire sequencing" (AIRR-seq or Rep-Seq). AIRR Community has been actively working to standardize protocols, metadata, formats, APIs, and other guidelines to promote open and reproducible studies of immune repertoire.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

Part of AIRR Data Model, describes abstract organizational unit of analysis that is defined by researcher and consists of study metadata, subject metadata, sample metadata, cell processing metadata, nucleic acid processing metadata, sequencing run metadata, set of raw sequence files, data processing metadata, and set of Rearrangements. Repertoire gathers all of this information together into composite object, which can be easily accessed by computer programs for data entry, analysis and visualization. AIRR Repertoire Schema has been implemented in YAML/JSON, which provides mechanism to share AIRR Repertoire metadata between research projects.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

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.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

Provides programmatic access to query and download AIRR-seq data. ADC API uses JSON as its communication format, and standard HTTP methods like GET and POST. ADC API is read only and mechanism of inclusion of AIRR-seq studies into data repository is left up to repository. ADC API Specification explains how to construct and execute API requests and interpret API responses.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

Encyclopedia of white and brown adipocyte secretome in mouse models and humans as key prerequisite to elucidating role of these mediators in normal physiology and disease.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

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.

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• RRID
• 4 years ago - submitted by Edyta Vieth

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.

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• RRID
• 4 years ago - submitted by Edyta Vieth

Wireless and fully standalone professional 3D scanner with new NVIDIA Jetson TX2 processor onboard. 3D scanning solution for data capture.

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• RRID
• 4 years ago - submitted by Edyta Vieth

Open source, community curated registry, meta-registry, and compact identifier resolver. Used for unifying identification of biomedical entities through integrative, open,community driven metaregistry. The registry contains metadata about ontologies, controlled vocabularies, and resources including their preferred prefix, name, description, homepage, mappings to other registries, and more.

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• RRID
• 4 years ago - submitted by Charles Hoyt

Provides analysis of biological, palaeontological and geological objects using computer assisted methods. Center for research at museum and for digitisation of scientific collections. Open to external users. In addition to various devices for three dimensional scanning, laboratory has workstations for processing and analysing raw data using 3D volume processing software.

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• RRID
• 4 years ago - submitted by Edyta Vieth

Nanofocus computed tomography system for applications in material science, precision injection moulding, micromechanics, electronics geology and biology. System includes nanofocus X-ray tube, precision mechanics and advanced software modules. Used for range of 3D CT applications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• RRID
• 4 years ago - submitted by Kristin Mahlow-Tillack

Web tool to predict effects of sequence variants on alternative splicing. Predicts changes in alternative 5' splice events as well as skipped exon events.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

Database for exploration of single cell RNA sequencing experiments from mouse and human. Collects and integrate data from multiple studies and present them through unified framework.

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• RRID
• 4 years ago - by Anonymous

Software package to provide functions richGO, richKEGG,and enrich to do functional enrichment analysis. Used for function enrichment analysis and network construction.

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• RRID
• 4 years ago - by Anonymous

Software R package to detect gene level differential selection between two groups of samples.Used for calculation of excess of non synonymous mutations between two groups.

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• ADC
• 4 years ago - by Anonymous

Software platform to integrate transcription factor gene interactions and validate regulatory networks. Gene regulatory network validation.

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• RRID
• 4 years ago - by Anonymous

Software platform to support systems biology research. Integrates genomic data and provides visualization and analysis tools for exploration of genomic data. Provides tools to generate biological hypotheses.

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• RRID
• 4 years ago - by Anonymous

Software R package providing missing functionality to ggplot2 through extension system introduced with ggplot2 v2.0.0.

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• RRID
• 4 years ago - by Anonymous