Curator Dashboard

A software used for data analysis

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• 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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• 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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• 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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• 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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• 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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• 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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• 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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• 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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• 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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• 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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• 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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• 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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• 1 year ago - by Anonymous

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

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• 1 year ago - by Anonymous

Biotechnology company to research and develop cell products for experimental use. Provides normal human and animal cells, cell culture media and reagents, gene analysis tools, cell-derived molecular biology products, cell-based assay kits, and stem cell products for research community. Focused on studying and developing cell therapeutic strategies to significantly improve quality of life for patients with degenerative diseases.

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• 1 year ago - by Anonymous

Software package called illustrator of biological sequences. Can be used for representing organization of either protein or nucleotide sequences. Multiple options are provided, and biological sequences can be manipulated, recolored or rescaled in user-defined mode. Final representational artwork can be directly exported into publication-quality figure. Used as illustrator for presentation and visualization of biological sequences. Standalone package was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available

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• 1 year ago - submitted by Shunhua Long

Software suite is designed to be of help when working with Human Genome Variation Society sequence variant nomenclature descriptions.

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• 1 year ago - submitted by Shunhua Long

Leading-edge science and technologies in analytical and measuring instruments including chromatographs and mass spectrometry. Manufactures precision instruments, measuring instruments and medical equipment.

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• 1 year ago - by Anonymous

Heavy duty, motorized microtome that can section large specimens with high quality. It's designed to be ergonomic and comfortable to use. Used for precise sectioning of hard and paraffin specimens in research, clinical, and industrial labs.

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• 1 year ago - by Anonymous

System provides ProFlow technology for nano-flow applications and is designed to provide high resolution, speed, and sensitivity for low-flow LC or LCMS applications, such as proteomics and metabolomics. It has wide flow-pressure footprint that supports nano, capillary, and micro applications.

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• 1 year ago - by Anonymous