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https://github.com/ABCD-STUDY/Minimally-Processed-Image-Sharing
Software to share ABCD minimally processed data. It uploads minimally-processed MRI data to the NDA ( Non-Disclosure Agreement) ABCD (Adolescent Brain Cognitive Development) repository.
Proper citation: Minimally-Processed-Image-Sharing (RRID:SCR_016016) Copy
https://github.com/ABCD-STUDY/enroll
Software which provides a framework for the secure storage of Personal Identifyable Information (PII) for a multi-site longitudinal project centrally. Used in Adolescent Brain Cognitive Development (ABCD) Study.
Proper citation: enroll (RRID:SCR_016011) Copy
Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version.
Proper citation: BECA (RRID:SCR_015846) Copy
http://standage.github.io/AEGeAn
Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.
Proper citation: Aegean (RRID:SCR_015965) Copy
Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences).
Proper citation: Aevol (RRID:SCR_015966) Copy
http://www.alliancegenome.org/
Organization that aims to develop and maintain sustainable genome information resources to promote understanding of the genetic and genomic basis of human biology, health, and disease. The Alliance is composed of FlyBase, Mouse Genome Database (MGD), the Gene Ontology Consortium (GOC), Saccharomyces Genome Database (SGD), Rat Genome Database (RGD), WormBase, and the Zebrafish Information Network (ZFIN).
Proper citation: Alliance of Genome Resources (RRID:SCR_015850) Copy
https://github.com/EvolBioInf/andi
Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes.
Proper citation: andi (RRID:SCR_015971) Copy
https://github.com/ABCD-STUDY/tick-tock
Software for research study observation that visualizes study related events per day. Any event generating function sends a 'tick' event to this application which will be visible on this applications web-interface.
Proper citation: tick-tock (RRID:SCR_016023) Copy
https://bioinf.eva.mpg.de/anfo/
Software for short read alignment and mapping of sequencing reads where the DNA sequence is somehow modified and/or there is more divergence between sample and reference than what fast mappers will handle.
Proper citation: Anfo (RRID:SCR_015972) Copy
https://github.com/ABCD-STUDY/FIONA-protocol-compliance
Software that contains multiple sequential lines of MATLAB commands and function calls for numerical computing for ABCD study protocol compliance.
Proper citation: FIONA-protocol-compliance (RRID:SCR_016027) Copy
https://github.com/ABCD-STUDY/Fast-Track-Image-Sharing
Software for sharing the ABCD (Adolescent Brain Cognitive Development) study data on the National Data Archive (NDA).
Proper citation: Fast-Track-Image-Sharing (RRID:SCR_016021) Copy
https://github.com/ABCD-STUDY/eprime-data-clean
Software to convert E-Prime (software tool for psychology computerized experiment design, data collection, and analysis) generated files to CSV files without errors during conversion. The ABCD project is using E-Prime to run behavioral tests.
Proper citation: eprime-data-clean (RRID:SCR_016020) Copy
https://funricegenes.github.io/
Dataset of functionally characterized rice genes and members of different gene families. The dataset was created by integrating data from available databases and reviewing publications of rice functional genomic studies.
Proper citation: funRiceGenes (RRID:SCR_015778) Copy
Community portal for a distributed data sharing platform and open protocol for building apps. The Dat Project imagines a web of commons created by global communities on open and secure protocols.
Proper citation: Dat Project (RRID:SCR_015779) Copy
http://apps.cytoscape.org/apps/cluepedia
Data analysis software and search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data and investigates interrelations within each pathway to reveal associations through gene/protein/miRNA enrichments.
Proper citation: CluePedia Cytoscape plugin (RRID:SCR_015784) Copy
https://en.freedownloadmanager.org/Windows-PC/Flowing-Software-FREE.html
Software for flow cytometry data analysis. Flowing Software has many common analysis tools, such as dot plots, histograms, quadrants, statistics, overlay histograms etc.
Proper citation: Flowing Software 2.5.1 (RRID:SCR_015781) Copy
University in Durham, England.
Proper citation: Durham University; Durham; England (RRID:SCR_016079) Copy
http://disulfind.dsi.unifi.it/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks.
Proper citation: DISULFIND (RRID:SCR_016072) Copy
https://github.com/boutiques/boutiques/
Software toolkit for a cross-platform JSON-framework for describing command-line tools and their parameters. It is accompanied by a Python tool which facilitates the creation, validation, simulation, execution, publishing, evaluation, and testing of tools described in this format.
Proper citation: Boutiques (RRID:SCR_016073) Copy
https://bitbucket.org/vboza/deepnano
Software for an alternative basecaller for DNA base calling in the portable Oxford Nanopore MinION sequencing device, based on deep recurrent neural networks. Used to improve base calling accuracy and reduce sequencing error rate.
Proper citation: DeepNano (RRID:SCR_016070) Copy
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