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XDec (Computational Deconvolution Tool)
Description of XDec
XDec deconvolutes small RNA-seq data from complex biofluids or fractions to estimate the exRNA expression profiles of constituent cargo profiles as well as the per-sample proportions of each constituent cargo profile.
Output from XDec includes:
- Stage 1 Deconvolution Results
- Stage1_Results_Boxplots.pdf - Boxplots of the per-sample proportions for each estimated constituent cargo profile (rows) numbered 1 through k. Boxplots are separated based on metadata columns (e.g., disease, biofluid, etc.).
- Stage1_Results_Expression.txt - exRNA expression in transformed transcript abundance values (rows) for each estimated constituent cargo profile (columns) numbered 1 through k (profiles modeled for the input dataset).
- Stage1_Results_Heatmap_Correlations.pdf - Estimated constituent cargo profiles (rows) are correlated using the exRNA expression in transformed transcript abundance values across the informative RNAs (see Murillo et al., 2019) against the 6 CTs (columns) previously identified through the deconvolution of the exRNA Atlas (see Murillo et al., 2019).
- Stage1_Results_Heatmap_Proportions.pdf - Heatmap of the per-sample proportions (columns) for each estimated constituent cargo profile (rows) numbered 1 through k. Dendrogram is included to cluster similar composed samples.
- Stage1_Results_Proportions.txt - Per-sample proportions (columns) for each estimated constituent cargo profile (rows) numbered 1 through k (profiles modeled for the input dataset).
- Stage 2 Deconvolution Results
- NOTE: Stage 2 deconvolution is performed for each metadata value that is associated with at least 20 samples.
- Stage2_[METADATA COLUMN]_[METADATA VALUE]_miRNA_RPM.txt - Tables of estimated average cargo profiles across miRNA transcripts in reads per million (rows) separated based on provided metadata values. Columns include mean expression and std. errors for each estimated constituent cargo profile (numbered 1 through k) as well as degrees of freedom, explained variances, and per sample residuals.
A full description of the deconvolution method used by XDec can be found in the Cell paper "ExRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present Across Human Biofluids" (Murillo et al., 2019).
There are three ways to use XDec:
- Submit your small RNA-seq biofluid data to the exRNA Atlas. We will deconvolute your data before releasing it to the public. By contributing your data to the exRNA Atlas, you will be providing new insights into exRNA biology for the wider scientific community and publicizing your own research in one of the largest web repositories for exRNA data. To learn more, read the guide on submitting data (and accompanying metadata) to the Atlas. You can also view existing deconvoluted Atlas datasets on the Public Analysis Results page.
- Use the Genboree Workbench, a web platform that hosts a variety of bioinformatics tools and stores related data for users, for your own private analyses. To learn more, read the guide.
- Install the exceRpt pipeline and XDec on your own private machine.