Curator Dashboard

Provides Prism softwares and services that integrate advanced imaging into the clinical workflow for brain mapping from acquisition through processing, visualization, and export to PACS. Prism integrates functional MRI, diffusion MRI, perfusion, MR spectroscopy, and PET/CT into a unified workflow for diagnosis and treatment planning in brain disorders. Processing is also available as a cloud deployed service, Prism Serve. Research support includes import/export for imaging and derived quantitative data in both DICOM and research formats such as AFNI and Trackviz.

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• RRID-Legacy
• 8 years ago - by Anonymous

Software R package for analysis of Affymetrix Data. Contains samples data files of a large size.

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• RRID-Legacy
• 8 years ago - by Anonymous

Web interface for computational prediction of nuclear hormone receptor binding sites in genomic sequences. Flexible Hidden Markov Model framework to allow for variable spacing and orientation of half sites. Allows for parameter modifications.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool to create and provide heat maps through a graphical interface. Allows to create an expression, pairwise comparison, image overlay, geomap, and geocoordinate heat maps for different data types and applications. Used to interactively visualize data.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

American multinational corporation and technology company headquartered in Santa Clara, California, in the Silicon Valley. Semiconductor chip maker being overtaken by Samsung. Inventor of the x86 series of microprocessors, the processors found in most personal computers (PCs). Intel supplies processors for computer system manufacturers such as Apple, Lenovo, HP, and Dell. Intel also manufactures motherboard chipsets, network interface controllers and integrated circuits, flash memory, graphics chips, embedded processors and other devices related to communications and computing.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Commercial organization providing laboratory solutions in the fields of psychophysiology, neuroscience, social science, life science, child and behavioral development. Offers a wide array of products and services including signal acquisition hardware used to collect a variety of measures including Cardiac Impedance, HRV, GSR/GSC, ECG/EKG, HR, BP, and EMG supplemented with software suite of analysis applications.

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• RRID-Legacy
• 8 years ago - by Anonymous

Software tool for generic streaming read processing tasks that have low memory or computational demands, such as format conversion, sub sampling, and various filtering operations.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool to merge two overlapping paired reads into a single read. Used in amplicon studies and in assembly, where longer reads allow the use of longer kmers or fewer comparisons.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool for trimming and filtering sequencing data. Used to combine data quality related trimming, filtering, and masking operations into a single tool adapter. BBDuk2 allows multiple kmer based operations in a single pass.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software suite of bioinformatics tools for analysis of DNA and RNA sequence data. Used for file formats such as fastq, fasta, sam, scarf, fasta plus qual, compressed or raw, with autodetection of quality encoding and interleaving. Written in Java and works on any platform supporting Java, including Linux, MacOS, and Microsoft Windows.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool for finding and removing adapters from Oxford Nanopore reads.

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• SciCrunch
• 8 years ago - by Anonymous

Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data.

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• SciCrunch
• 8 years ago - by Anonymous

Software tool as a short read aligner for DNA and RNA seq data. Used for large genomes with millions of scaffolds. Can align reads from Illumina, PacBio, 454, Sanger, Ion Torrent, Nanopore. Fast and accurate, particularly with highly mutated genomes or reads with long indels, even whole gene deletions over 100kbp long. It has no upper limit to genome size or number of contigs. Written in Java, can run on any platform.

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• SciCrunch
• 8 years ago - by Anonymous

Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them.

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• RRID-Legacy
• 8 years ago - by Anonymous

Software tool to provide fast all in one preprocessing for FastQ files. Developed in C++ with multithreading supported to afford high performance. Performs quality control, adapter trimming, quality filtering, per read quality pruning and many other operations with a single scan of the FASTQ data.

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• SciCrunch
• 8 years ago - submitted by Julien Bane

Software tools to make developing R packages easier by providing R functions that simplify and expedite common tasks.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool as a full probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen.

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• SciCrunch
• 8 years ago - submitted by kristian hanghoej

Portal for Science Dynamics projects with open source framework to provide way to query datasets. Code framework, including tutorials for project, titled Over Optimization of Academic Publishing Metrics Observing Goodhart Law in Action, to interactively explore and understand how various properties of journals have changed over time. Datasets, software implementations, code tutorials and interactive web interface for investigating studied networks.

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• SciCrunch
• 8 years ago - submitted by Michael Fire