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Introduction |
Welcome to CANDELbio! Our documentation is still very much a work in progress.
The CANDEL Platform encompasses the universe of tools we use to store, analyze, query and plot data. This includes the CANDEL database itself!
- luminance: visualize data from CANDEL
- workerbee: process your data for ingestion into CANDEL
- wick: get data out of CANDEL in a table format
- datalogr: generate custom queries for CANDEL
- glow: deploy a shiny UI for visualization of a CANDEL project
The CANDEL database is where most useable data lives in the form of measurements linked to relevant sample metadata and patient clinical data.
To see what kind of data we keep in CANDEL, try checking out the schema, which is explained in great detail here.
Enflame is a visual query builder for the CANDEL dabase. You can construct a query by combining blocks. You can then run the query against a selected CANDEL database, or you can take the generated text representation of it in wick, and include it in your own code. Enflame also includes the ability to do some simple data visualization on the returned data, also by using blocks and block structure (see Visualization blocks).
Rawsugar is PICI՚s tool for raw data ingestion, storage, and retrieval. The user guide for rawsugar can be found here and will walk you through ingesting and organizing raw data in rawsugar!
Mantis Viewer is an application for viewing and analyzing multi-channel pathology imaging, such as IHC, Vectra, MIBI, IMC, CODEX, or other technologies. It has been designed to be highly performant and responsive when analyzing both large and small images and to support workflows with segmentation data.
Terra is a cloud based workflow runner developed by the Broad Institute for handing large genomics pipelines in parallel. We use it for Because it runs off of docker images, we can use it for much more than genomics work, including segmentation of cells in images.