ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells.
Immune cell infiltration of tumors and the tumor microenvironment can be an important component for determining patient outcomes. For example, immune and stromal cell presence inferred by deconvolving patient gene expression data may help identify high risk patients or suggest a course of treatment....
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2019-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0224693 |
| _version_ | 1818919191687725056 |
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| author | Samuel A Danziger David L Gibbs Ilya Shmulevich Mark McConnell Matthew W B Trotter Frank Schmitz David J Reiss Alexander V Ratushny |
| author_facet | Samuel A Danziger David L Gibbs Ilya Shmulevich Mark McConnell Matthew W B Trotter Frank Schmitz David J Reiss Alexander V Ratushny |
| author_sort | Samuel A Danziger |
| collection | DOAJ |
| description | Immune cell infiltration of tumors and the tumor microenvironment can be an important component for determining patient outcomes. For example, immune and stromal cell presence inferred by deconvolving patient gene expression data may help identify high risk patients or suggest a course of treatment. One particularly powerful family of deconvolution techniques uses signature matrices of genes that uniquely identify each cell type as determined from single cell type purified gene expression data. Many methods from this family have been recently published, often including new signature matrices appropriate for a single purpose, such as investigating a specific type of tumor. The package ADAPTS helps users make the most of this expanding knowledge base by introducing a framework for cell type deconvolution. ADAPTS implements modular tools for customizing signature matrices for new tissue types by adding custom cell types or building new matrices de novo, including from single cell RNAseq data. It includes a common interface to several popular deconvolution algorithms that use a signature matrix to estimate the proportion of cell types present in heterogenous samples. ADAPTS also implements a novel method for clustering cell types into groups that are difficult to distinguish by deconvolution and then re-splitting those clusters using hierarchical deconvolution. We demonstrate that the techniques implemented in ADAPTS improve the ability to reconstruct the cell types present in a single cell RNAseq data set in a blind predictive analysis. ADAPTS is currently available for use in R on CRAN and GitHub. |
| first_indexed | 2024-12-20T01:01:56Z |
| format | Article |
| id | doaj.art-c210f3640b084ae4b0efafef16177ca4 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-20T01:01:56Z |
| publishDate | 2019-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-c210f3640b084ae4b0efafef16177ca42022-12-21T19:58:58ZengPublic Library of Science (PLoS)PLoS ONE1932-62032019-01-011411e022469310.1371/journal.pone.0224693ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells.Samuel A DanzigerDavid L GibbsIlya ShmulevichMark McConnellMatthew W B TrotterFrank SchmitzDavid J ReissAlexander V RatushnyImmune cell infiltration of tumors and the tumor microenvironment can be an important component for determining patient outcomes. For example, immune and stromal cell presence inferred by deconvolving patient gene expression data may help identify high risk patients or suggest a course of treatment. One particularly powerful family of deconvolution techniques uses signature matrices of genes that uniquely identify each cell type as determined from single cell type purified gene expression data. Many methods from this family have been recently published, often including new signature matrices appropriate for a single purpose, such as investigating a specific type of tumor. The package ADAPTS helps users make the most of this expanding knowledge base by introducing a framework for cell type deconvolution. ADAPTS implements modular tools for customizing signature matrices for new tissue types by adding custom cell types or building new matrices de novo, including from single cell RNAseq data. It includes a common interface to several popular deconvolution algorithms that use a signature matrix to estimate the proportion of cell types present in heterogenous samples. ADAPTS also implements a novel method for clustering cell types into groups that are difficult to distinguish by deconvolution and then re-splitting those clusters using hierarchical deconvolution. We demonstrate that the techniques implemented in ADAPTS improve the ability to reconstruct the cell types present in a single cell RNAseq data set in a blind predictive analysis. ADAPTS is currently available for use in R on CRAN and GitHub.https://doi.org/10.1371/journal.pone.0224693 |
| spellingShingle | Samuel A Danziger David L Gibbs Ilya Shmulevich Mark McConnell Matthew W B Trotter Frank Schmitz David J Reiss Alexander V Ratushny ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells. PLoS ONE |
| title | ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells. |
| title_full | ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells. |
| title_fullStr | ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells. |
| title_full_unstemmed | ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells. |
| title_short | ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells. |
| title_sort | adapts automated deconvolution augmentation of profiles for tissue specific cells |
| url | https://doi.org/10.1371/journal.pone.0224693 |
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