Identifier Refinery Conversion Matrixes

identifier-refinery

Tools and assets for easy and reproducable gene identifier conversion.

Methods

This repository is used to build matricies which can convert between different gene identifiers.

These conversion matricies are built by:

• Randomly choosing raw CEL files from NCBI GEO for a given platform accession code (in /cels)
• Reading the CEL header and joining Brainarray (e.g., hgu133plus2hsensgprobe) and Bioconductor (e.g., hgu133plus2.db) (x, y) coordinates
• Finding intersecting probe identifiers
• Extracting supported identifiers and probe IDs from the Bioconductor package
• Filtering on probe IDs and Ensembl Gene IDs in Brainarray
• Writing the output to a conversion TSV file
• Check that all output conversion TSV files have a shared SHA1

Repository Contents

Source Files

The cels directory contains raw CEL files taken from GEO. The list of supported platforms is in supported_microarray_platforms.csv. Source files can be acquired by running the acquire_cels.py script.

Docker Image

The conversion scripts are run on custom Docker images.

Two Dockerfiles are provided in this repository - base Docker image, which is used to install the quire R dependancies, and the pd image, which is used to build the required databases for a given platform.

Conversion Scripts

A build_and_convert.py script is provided, which build a unique Docker image for each package, mount the downloaded CEL files as a volume, and then run the gene conversion script R/gene_convert.R inside the image and output the master conversion matrix. Output TSV files live in cels/out/.

Reproducing

The entire process can be reproduced by running the following command script from a fresh checkout of this repository. It will take some time:

$ ./generate_matricies_from_scratch.sh

You can also choose to only build a specific platform, ex.,:

$ ./generate_matricies_from_scratch.sh celegans

Identifiers

Released assets in this repository are availble under the DOI, xyz:1.2.3.4, which can be seen on Zenodo here.

Related Projects

• AlexsLemonade/refinebio

Copyright

identifier-refinery output assets are released under a CC0 1.0 Universal license. All code is released under the BSD 3-clause license. Input assets are property of the original providers to NCBI GEO, but may be freely downloaded and redistributed unless otherwise noted.

https://github.com/AlexsLemonade/identifier-refinery