| Title: | Orchestrating Blood Radiation Transcriptomic Data |
|---|---|
| Description: | DoReMiTra is an R data package providing access to curated transcriptomic datasets related to blood radiation, with a focus on neutron, x-ray, and gamma ray studies. It is designed to facilitate radiation biology research and support data exploration and reproducibility in radiation transcriptomics. All datasets are provided as SummarizedExperiment objects, allowing seamless integration with the Bioconductor ecosystem. |
| Authors: | Ahmed Salah [aut, cre] (ORCID: <https://orcid.org/0000-0001-7003-4466>), Federico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>) |
| Maintainer: | Ahmed Salah <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.2.0 |
| Built: | 2026-10-10 11:19:59 UTC |
| Source: | https://github.com/bioc/DoReMiTra |
This function compares the essential metadata information of 2 or more SE objects including radiation type, dose, time point, etc.
compare_DoReMiTra_datasets( se_list, fields = c("Radiation_type", "Dose", "Sex", "Time_point", "Organism", "Tissue") )compare_DoReMiTra_datasets( se_list, fields = c("Radiation_type", "Dose", "Sex", "Time_point", "Organism", "Tissue") )
se_list |
names of the se objects to be compared |
fields |
a character vector of the main metadata info |
a dataframe comparing the metadata of the selected datasets
se1 <- get_DoReMiTra_data("SE_Paul_2010_InVivo_GSE23393_GPL6480") se2 <- get_DoReMiTra_data("SE_Amundson_2011_InVivo_GSE20162_GPL6480") se_list<- list(Amundson = se1, Paul= se2) compare_DoReMiTra_datasets(se_list = se_list)se1 <- get_DoReMiTra_data("SE_Paul_2010_InVivo_GSE23393_GPL6480") se2 <- get_DoReMiTra_data("SE_Amundson_2011_InVivo_GSE20162_GPL6480") se_list<- list(Amundson = se1, Paul= se2) compare_DoReMiTra_datasets(se_list = se_list)
Retrieves all datasets available in the DoReMiTra package from ExperimentHub
and returns them as a named list of SummarizedExperiment objects. This is
useful for batch processing or exploring all curated radiation response datasets
at once.
get_all_DoReMiTra_datasets(verbose = TRUE)get_all_DoReMiTra_datasets(verbose = TRUE)
verbose |
Logical. Whether to print progress messages. Default is TRUE. |
A list storing all the SE objects
get_all_DoReMiTra_datasets()get_all_DoReMiTra_datasets()
This function fetches a SummarizedExperiment object from ExperimentHub
corresponding to a dataset in the DoReMiTra package.
get_DoReMiTra_data(dataset_name, gene_symbol = FALSE)get_DoReMiTra_data(dataset_name, gene_symbol = FALSE)
dataset_name |
Character. The exact name of the dataset (e.g. "SE_Amundson_2008_ExVivo_GSE8917_GPL1708"). |
gene_symbol |
Logical. default is FALSE. If TRUE, gene symbol will be assigned to rownames. If some gene symbols were found to be duplicated, gene symbol and the corresponding probe id will be appended together. |
A SummarizedExperiment object fetched from ExperimentHub.
get_DoReMiTra_data("SE_Amundson_2008_ExVivo_GSE8917_GPL1708")get_DoReMiTra_data("SE_Amundson_2008_ExVivo_GSE8917_GPL1708")
Returns a metadata dataframe of all datasets available in the DoReMiTra collection, including details such as title, organism, radiation type, experimental setting, author, and accession numbers. Can optionally display extended metadata fields.
list_DoReMiTra_datasets(show_all_fields = FALSE)list_DoReMiTra_datasets(show_all_fields = FALSE)
show_all_fields |
Logical. If TRUE, it returns all the metadata information |
A data.frame with metadata for each dataset
list_DoReMiTra_datasets()list_DoReMiTra_datasets()
This function displays the available metadata fields across all DoReMiTra datasets along with the unique values observed for each field. It facilitates intuitive dataset discovery and filtering.
list_DoReMiTra_metadata_fields()list_DoReMiTra_metadata_fields()
Invisibly returns a named list of metadata fields and their values.
list_DoReMiTra_metadata_fields()list_DoReMiTra_metadata_fields()
Filters the available DoReMiTra datasets using metadata fields such as radiation type, organism, or experimental setting. This function helps narrow down datasets of interest before fetching them.
search_DoReMiTra_datasets( radiation_type = NULL, organism = NULL, exp_setting = NULL, author = NULL )search_DoReMiTra_datasets( radiation_type = NULL, organism = NULL, exp_setting = NULL, author = NULL )
radiation_type |
Character string (optional). Filter datasets by radiation type (e.g., "x-ray", "neutron"). |
organism |
Character string (optional). Filter by organism (e.g., "Homo sapiens"). |
exp_setting |
Character string (optional). Filter by experimental setting (e.g., "in vivo", "ex vivo"). |
author |
Character string (optional). Filter by the author name |
a vector with the names of the se objects matching the inclusion criteria. If none match, returns an empty vector with a message.
search_DoReMiTra_datasets()search_DoReMiTra_datasets()
#' Provides a concise overview of a SummarizedExperiment object from the DoReMiTra collection.
Displays information such as the number of samples, metadata content, and
key experimental conditions like radiation type, organism, and platform.
summarize_DoReMiTra_se(se)summarize_DoReMiTra_se(se)
se |
The name of the SE object as defined by the user |
A character string containing a essential information about the dataset metadata
se <- get_DoReMiTra_data("SE_Ghandhi_2018_InVivo_GSE84898_GPL13497") summarize_DoReMiTra_se(se)se <- get_DoReMiTra_data("SE_Ghandhi_2018_InVivo_GSE84898_GPL13497") summarize_DoReMiTra_se(se)