Curator Dashboard

Core answers research questions in any scientific, medical or industrial discipline through capture, processing, image analysis, training and sample preparation services for microscopy. Provides technical and scientific support in advanced microscopy and image processing and analysis.

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• SciCrunch
• 1 year ago - submitted by Edyta Vieth

Core offers Next Generation Sequencing services using Element Biosciences AVITI short read sequencer, PacBio Revio and Oxford Nanopore Promethion/GridIon long read sequencers along with 10X Genomics X, 10X Genomics Visium CytAssist, and 10X Xenium Analyzer single cell/spatial technologies.

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• SciCrunch
• 1 year ago - submitted by Edyta Vieth

Research institute in Esch-sur-Alzette, Luxembourg to study brain and its diseases. Collaboration between biologists, medical and computer scientists, physicists, engineers as well as mathematicians offers new insights into complex biological mechanisms and disease processes, with the aim of developing new tools for diagnostics, prevention, and therapy. LCSB has established strategic partnerships with scientific partners worldwide and with all major biomedical research units in Luxembourg. Carries out collaborative projects with hospitals and research-oriented companies, accelerating translation of fundamental research results into clinical applications.

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• RRID
• 1 year ago - by Anonymous

Software package provides framework of functions and shiny-applications to work with spatial expression data. Used for spatial transcriptomics analysis.

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• RRID
• 1 year ago - submitted by Balagopal Pai

Search for variants, CNVs, genes, transcripts, publications, diseases.

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• RRID
• 1 year ago - submitted by Shunhua Long

Web service to search for variants, CNVs, genes, transcripts, publications, diseases. Annotation tool and search engine for human genomic variants, and platform enabling sharing of knowledge on specific variants. Enables users to look up variants in their genomic context, collects data from multiple databases in central location and most importantly, aims to enable community to freely and easily share knowledge on human variation.

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• RRID
• 1 year ago - by Anonymous

A software used for data analysis

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• RRID
• 1 year ago - submitted by Ebrahim Mohammed

Software R package for single cell and other data analysis using diffusion maps. Package for diffusion maps, with additional features for large-scale and single cell data.

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• RRID
• 1 year ago - by Anonymous

Software tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from fluid and solid tissues, including tumors. Performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 and reports consensus contigs of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to identify the corresponding gene and CDR3 details. TRUST4 supports both single-end and paired-end bulk or single-cell sequencing data with any read length.

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• RRID
• 1 year ago - by Anonymous

Shared high-performance computing cluster. All research teams on Sherlock have access to a base set of managed computing resources, GPU-based servers, and a multi-petabyte, high-performance parallel file system for short-term storage. Stanford Faculty can supplement these shared nodes by purchasing additional servers. By investing in the cluster, PI groups not only receive exclusive access to the nodes they purchase, but also get access to all the other owner compute nodes when they're not in use, thus giving them access to the whole breadth of Sherlock resources.

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• RRID
• 1 year ago - by Anonymous

Deep learnining based variational inference method to integrate scRNA-seq with spatial transcriptomics data. ENVI learns to reconstruct spatial onto for dissociated scRNA-seq data and impute unimagd genes onto spatial data.

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• RRID
• 1 year ago - by Anonymous

Deep learning framework, with support for JAX, TensorFlow, and PyTorch. Used to build and train models for computer vision, natural language processing, audio processing, timeseries forecasting, recommender systems. Offers consistent and simple APIs, minimizes number of user actions required for common use cases, and provides clear and actionable error messages. Keras also gives the highest priority to crafting documentation and developer guides.

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• RRID
• 1 year ago - by Anonymous

Software pipeline that simultaneously collects and processes Xenium In Situ Gene Expression data. Used for analyzing and visualizing in situ gene expression data produced by the Xenium Analyzer.

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• RRID
• 1 year ago - by Anonymous

Software tool for analysis and visualization of spatial molecular data. Scalable framework for spatial omics analysis. Builds on top of scanpy and anndata, from which it inherits modularity and scalability. Provides analysis tools that leverages spatial coordinates of data, as well as tissue images.

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• RRID
• 1 year ago - by Anonymous

Software framework for processing spatial omics data. Data framework that comprises FAIR storage format and collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets.

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• RRID
• 1 year ago - by Anonymous

Database that aims to comprehensively explore distinct functional states of cancer cells at the single-cell level. Provides functional state-associated PCG/lncRNA repertoires across all cancers, in specific cancers, and in individual cancer single-cell datasets. Provides interface for comprehensively searching, browsing, visualizing and downloading functional state activity profiles of cancer single cells and corresponding PCGs/lncRNAs expression profiles.

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• RRID
• 1 year ago - by Anonymous

Enhanced web server for large-scale expression profiling and interactive analysis. GEPIA2 is updated and enhanced version of GEPIA, offering more functionalities, higher resolution data analysis, and additional features like ability to analyze specific cancer subtypes, quantify gene signatures based on single-cell sequencing studies, and allow users to upload their own RNA-seq data for comparison with the TCGA and GTEx datasets; essentially providing more comprehensive and advanced platform for gene expression analysis compared to the original GEPIA version.

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• RRID
• 1 year ago - by Anonymous

Software application used with Bruker's atomic force microscopes and scanning probe microscopes. Software package for analyzing SPM data including images, ramp data, HSDC data, collected using Bruker SPMs.

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• RRID
• 1 year ago - by Anonymous

Software used for quantitative Western blot imaging and analysis. Designed to look at multiple proteins simultaneously on single assay. This software is sensitive enough to distinguish co-migrating proteins, such as phosphorylated and unphosphorylated.

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• RRID
• 1 year ago - by Anonymous

Software Galaxy tools dedicated to ecology data management and analysis, available through Galaxy Tool Shed.

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• RRID
• 1 year ago - by Anonymous