Curator Dashboard

Software tool for assignment of known mutational signatures to individual samples and individual somatic mutations.

• Resource
• RRID
• 1 year ago - by Anonymous

Software tool to identify genomic structural variation in target regions/genes from reference-aligned high-throughput sequence data. Used to identify structural variation from sequencing data in target regions.

• Resource
• RRID
• 1 year ago - by Anonymous

Software tool to predict completeness and contamination of genomic bins. Used for predicting genome quality of metagenome-assembled genomes. Assessing microbial genome quality using machine learning.

• Resource
• RRID
• 1 year ago - by Anonymous

Software command tool for metagenomic binning with deep learning, handles both short and long reads. Used for metagenomic binning at contig level which uses deep contrastive learning.

• Resource
• RRID
• 1 year ago - by Anonymous

Ultrasonicator is scalable, automated high-performance sample preparation instrument with automated water works to optimize user-to-user reproducibility and remote set-up and scheduling. Designed for integration with high-throughput laboratory automation. Includes integrated AFA ultraCUBE water chiller and water conditioning module.

• Resource
• RRID
• 1 year ago - submitted by Tito Sandoval

Fully-automated, widefield cell imaging system. Building on capabilities of earlier IN Cell Analyzer systems, it provides platform to deliver advances in speed, image quality, and throughput. Allows to perform analysis.

• Resource
• RRID
• 1 year ago - submitted by Kyriaki-Barbara Papalois

AI-powered scanner for H&E- and IHC-stained whole slide images that enables automated quality control workflow by detecting the most common artifacts generated during process of slide preparation and scanning including air bubbles, dust/debris, folds, out-of-focus areas, and pen marks. It is integrated into the HALO AP diagnostic digital pathology platform.

• Resource
• RRID
• 1 year ago - submitted by Kyriaki-Barbara Papalois

Immunohistochemistry stainer is united with software and connectivity options. Can process 48 slides in less than three hours.

• Resource
• RRID
• 1 year ago - submitted by Kyriaki-Barbara Papalois

Bench-standing IHC/ISH stainer with three-tray system, with 3.5hour run times. Each tray functions independently, allowing on-demand access and enabling you to load slides as they become available. System accommodates up to 29 antibodies (with detection loaded) and allows for easy swapping of antibodies without interrupting ongoing staining processes.

• Resource
• RRID
• 1 year ago - submitted by Kyriaki-Barbara Papalois

Qubit fluorometer designed to accurately measure DNA, RNA, and protein quantity, and now also RNA integrity and quality. Qubit 4 Fluorometer was re-engineered to enable data transfer via WiFi as well as to run Qubit RNA IQ assay. Qubit 4 Fluorometer and RNA IQ Assay Kit work together to accurately distinguish intact from degraded RNA in two steps.

• Resource
• RRID
• 1 year ago - submitted by Kyriaki-Barbara Papalois

Database compiles various types of data and information from literature and generalist databases on human TP53 gene variations related to cancer.

• Resource
• RRID
• 1 year ago - by Anonymous

Software R package with various confidence intervals for binomial proportions inside. Confidence intervals are for single, paired and independent proportions. Various confidence interval methods for proportions.

• Resource
• RRID
• 1 year ago - by Anonymous

High-performance computing facility. Its resources have been designed to support labs engaged in genetics and bioinformatics research, but are open to anyone on campus. The Stanford SCG Bioinformatics Cluster is optimized to support large memory, single-node threaded applications as well as applications and workflows that require many small files.

• Resource
• RRID
• 1 year ago - submitted by A. Karl Kornel

Software R package provides two methods of plotting categorical scatter plots such that arrangement of points within category reflects the density of data at that region, and avoids over-plotting. Categorical Scatter (Violin Point) Plots.

• Resource
• RRID
• 1 year ago - by Anonymous

Software R package to convert statistical analysis objects from R into tidy format. Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once.

• Resource
• RRID
• 1 year ago - by Anonymous

Code to analyse data from "Conserved pan-cancer microenvironment subtypes predict response to immunotherapy" by Bagaev et al.

• Resource
• RRID
• 1 year ago - by Anonymous

Software package contains all original code used to process MxIF data.

• Resource
• RRID
• 1 year ago - by Anonymous

Core provides imaging systems for advanced microscopy including confocal, multi-photon and super-resolution modalities, enabling users to address research questions in living systems across temporal and spatial scales. Staff offers training to use equipment, expertise about experimental strategy, design, image processing and analysis.

• Resource
• RRID
• 1 year ago - by Anonymous

Electronics Core is electronics design, development and repair facility which specializes in proof-of-concept design and prototyping, and early stage development of medical devices and laboratory research instrumentation. Services include system design, schematic capture, printed circuit board layout, board fabrication, assembly and testing.

• Resource
• RRID
• 1 year ago - submitted by Matthew Rudy

Core facility for synthetic biology experimentation including pilot-scale fermentation, high throughput automation, biological sample analysis, and cell-free protein synthesis.

• Resource
• RRID
• 1 year ago - by Anonymous