Multiomics configs is a Github repository that contains information and configuration files for reanalysis of proteomics, genomics and transcriptomics datasets. The current repository including the following sections:
Annotated datasets are divided into multiple categories, mainly absolute and differential expression.
Absolute expression datasets are datasets that aim to quantified absolute protein expression. Currently, datasets are devided into multiple categories:
- cell-lines
- platelet
- tissues
- tumor
The factor value for each absolute expression dataset should be the organism part (tissue) in tissue datasets or the cell-line code in the cell line datasets. In absolute expression profiles each dataset contains a global SDRF where all the samples are annotated (e.g. PXD000612). This representation allows to analyze the experiment complete or divided by samples.
Differential expression datasets are datasets that aim to quantified the diffenretial expressed proteins in specific diseases or conditions. Currently, datasets are divided into multiple categories taking to account the analytical method:
- label-free
- dia
- tmt
NOTE: For each dataset only one factor value should be added for each SDRF. If more than one variable is studied, then multiple SDRFs should be added with the following structure PXD-{factor value}.sdrf.tsv
If possible, creates the IDF for each dataset.
The Database folder contains multiple databases created for the reanalysis of data including UniProt, ENSEMBL, contaminants databases.
LFQ and TMT datasets are search against non-canonical and tissue specific variant databases generated with pgdb nextflow pipeline. The list of datasets can be found here
If you want to add a dataset to the repository please create a Pull request with the annotations.