Curator Dashboard

Software tool for microsatellite instability detection using high throughput sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region sequencing data as input. Introduces multinomial distribution model to quantify polymerase slippages for each tumor sample and discriminative sites selection method to enable MSI detection without matched normal samples.

• Resource
• RRID
• 2 years ago - by Anonymous

Open source platform to support management of educational audio and video content. Institutions can use Opencast to produce lecture recordings, manage existing video, serve designated distribution channels, and provide user interfaces to engage students with educational videos.

• Resource
• RRID
• 2 years ago - submitted by Manuel Oellers

Core utilizes dual tube micro X-ray computed tomography scanner for imaging specimens in fields of paleontology, comparative anatomy, evolution and development, basic biomedical studies, and research in geology and material sciences.It is equipped with 180 kV nano-focus and high power 240 kV micro-focus CT tube. This setup allows to scan very small specimens with high resolution using nano tube or dense fossils using high power tube.

• Resource
• SciCrunch
• 2 years ago - by Anonymous

Core provides bioinformatics and statistics expertise. Core develops and maintains automated and customizable workflows for processing and analyzing many types of genomic data; supports design of rigorous, robust and reproducible experiments and proposals; assists in preparation of manuscripts, grants and presentations; and provides education and training in use of software and analysis methods.Core can contribute to many types of bioinformatics or statistical projects.

• Resource
• SciCrunch
• 2 years ago - submitted by Edyta Vieth

Core is part of the University of Manchester Faculty of Science and Engineering. Facility offers support and services in chemistry, biology and materials. Mass spectrometers including Orbitraps, Ion Mobility, MALDI, DESI, hyphenated LC-MS and GC-MS apparatuses. Other instruments are HPLC systems, UHPLC systems and GC systems.

• Resource
• RRID
• 2 years ago - by Anonymous

Shared instrumentation facility at the American Museum of Natural History with tools for X-ray tomography, electron microscopy, confocal microscopy, light microscopy and image analysis. Provides expert assistance in the use of all lab equipment.

• Resource
• SciCrunch
• 2 years ago - by Anonymous

Software application to integrate scRNA-seq and scTCR-seq data to allow for more comprehensive analysis that leverages the strengths of both data types.Repository contains code and information of data used in the paper “scNAT: A deep learning method for integrating paired single cell RNA and T cell receptor sequencing profiles”. Source code for scNAT are in the scNAT folder, the tutorial is in the tutorials folder.

• Resource
• RRID
• 2 years ago - by Anonymous

Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats.

• Resource
• RRID
• 2 years ago - by Anonymous

Software pipeline for annotating predicted Nucleotide binding and leucine rich repeat genes from non-masked genome fasta file input.

• Resource
• RRID
• 2 years ago - by Anonymous

Software tool for joint surface based registration and atlas construction of brain geometry and function.Cortical registration framework that jointly models mismatch between geometry and function while simultaneously learning unbiased population specific atlas.

• Resource
• RRID
• 2 years ago - submitted by Anita Bandrowski

Japanese multi omics reference panel. Provides multidimensional approach to diversity of Japanese population. Public database for plasma metabolome and proteome analyses. Updated to metabolome, genome, transcriptome, metagenome, number of samples, analysis methods of each dataset, expanding links between each layer and links between hierarchies.

• Resource
• RRID
• 2 years ago - by Anonymous

Core provides access to genomic technologies and Next-Generation Sequencing. Provides DNA and RNA quality control services, user accessible instrumentation, training, consultation services, bioinformatics support, and secure data delivery management.

• Resource
• RRID
• 2 years ago - by Anonymous

Web application to transform Nutil outputs and plots it on mouse anatomical heatmap.

• Resource
• RRID
• 2 years ago - submitted by Lindsay Meyerdirk

Software C toolkit for alignment free and spatial temporal analysis of multi-FASTA data. Used for entangling presence of multiple sequences from epidemic and pandemic events.

• Resource
• RRID
• 2 years ago - submitted by Jorge da Silva

Software toolkit for analyzing spatial molecular data. Underlying framework is generalizable to spatial datasets mapped to XY coordinates. Package uses anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. Python based implementation efficiently deals with large datasets of millions of cells.

• Resource
• RRID
• 2 years ago - submitted by Sarah Arena

Software tools for interactive viewing and fast sharing of large image data. Comprises Minerva Author, a tool to create and annotate images, and Minerva Story, a narrative image viewer for web hosting. Used for interpreting and interacting with complex images, organized around guided analysis approach. Enables fast sharing of large image data that is stored on Amazon S3 and viewed using zoomable image viewer implemented using OpenSeadragon, making it ideal for integration into multi-omic browsers for data dissemination of tissue atlases.

• Resource
• SciCrunch
• 2 years ago - submitted by Han Xu

Core provides range of genomics technologies to support basic, translational, and clinical research.Services support basic research. Clinical assays offered are similar to those offered to support basic research, except that these assays are validated under CLIA, enabling them to be used in clinical decision making process in research protocols and for routine patient care.

• Resource
• SciCrunch
• 2 years ago - submitted by Edyta Vieth

Offers advanced imaging technology, as well as training and support personalized to their imaging goals and experience. Provides Technology access and training; Assisted imaging and coaching at every step of the imaging workflow, from sample preparation to data analysis; Pilot experiments and feasibility testing; Developing custom image analysis pipelines; Image analysis consultation and training; Developing and testing new instruments and devices; Full scientific and technological collaborations and partnerships; Offsite coaching, assistance and consulting ; Collaborative projects in academic, health and allied industrial sectors;

• Resource
• SciCrunch
• 2 years ago - submitted by Edyta Vieth

Software application provides simple MATLAB commands for creating and interconnecting layers of deep neural network.

• Resource
• RRID
• 2 years ago - by Anonymous

Web server to predict IL-10 inducing peptides, where users are allowed to paste or upload file with multiple peptide sequences and each sequence would be predicted according to model selected. Used to design, discover and mapping of peptides that may induce IL-10.

• Resource
• RRID
• 2 years ago - by Anonymous