DoReMiTra provides a curated resource of radiation transcriptomic datasets with harmonized metadata for cross-study comparison such as:
Radiation_type, either Xray, gamma ray, neutronDose, which is commonly measured in GyTime_point, normally indicating the time post radiation exposureSex of the donors/samples collectedOrganism, which at the current state of things is Homo sapiens and Mus musculusExp_setting exvivo invivoThe package delivers data as SummarizedExperiment objects directly accessible via ExperimentHub, enabling easy subsetting, filtering, and comparative analyses.
This vignette guides you through:
To install this package, start R and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("DoReMiTra")Once installed, the package can be loaded and attached to your current workspace as follows:
library("DoReMiTra")datasets <- list_DoReMiTra_datasets()
knitr::kable(datasets)| Dataset | RadiationType | Organism | ExpSetting | Accession |
|---|---|---|---|---|
| SE_Amundson_2019_InVivo_GSE124612_GPL11202 | gamma ray | Mus musculus | InVivo | GSE124612 |
| SE_Aryankalayil_2018_InVivo_GSE104121_GPL10787 | gamma ray | Mus musculus | InVivo | GSE104121 |
| SE_Aryankalayil_2018_InVivo_GSE104121_GPL21163 | gamma ray | Mus musculus | InVivo | GSE104121 |
| SE_Park_2017_ExVivo_GSE102971_GPL10332_MacacaMulatta | gamma ray | Macaca mulatta | ExVivo | GSE102971 |
| SE_Park_2017_ExVivo_GSE102971_GPL10332_HomoSapiens | gamma ray | Homo sapiens | ExVivo | GSE102971 |
| SE_Vasilyev_2017_ExVivo_GSE97000_GPL17077 | gamma ray | Homo sapiens | ExVivo | GSE97000 |
| SE_Paul_2013_ExVivo_GSE44201_GPL6480 | gamma ray | Homo sapiens | ExVivo | GSE44201 |
| SE_Paul_2013_ExVivo_GSE44201_GPL6848 | gamma ray | Homo sapiens | ExVivo | GSE44201 |
| SE_Nosel_2013_ExVivo_GSE43151_GPL13497 | gamma ray | Homo sapiens | ExVivo | GSE43151 |
| SE_Girardi_2012_ExVivo_GSE20173_GPL6480 | gamma ray | Homo sapiens | ExVivo | GSE20173 |
| SE_Amundson_2011_ExVivo_GSE23515_GPL6480 | gamma ray | Homo sapiens | ExVivo | GSE23515 |
| SE_Gruel_2008_ExVivo_GSE6978_GPL4803 | gamma ray | Homo sapiens | ExVivo | GSE6978 |
| SE_Rouchka_2019_ExVivo_GSE63952_GPL15207 | gamma ray | Homo sapiens | ExVivo | GSE63952 |
| SE_Amundson_2008_ExVivo_GSE8917_GPL1708 | gamma ray | Homo sapiens | ExVivo | GSE8917 |
| SE_Manikandan_2014_ExVivo_GSE36355_GPL6883 | gamma ray | Homo sapiens | ExVivo | GSE36355 |
| SE_Lee_2013_ExVivo_GSE44245_GPL570 | gamma ray | Homo sapiens | ExVivo | GSE44245 |
| SE_Rouchka_2015_ExVivo_GSE64375_GPL6244 | gamma ray | Homo sapiens | ExVivo | GSE64375 |
| SE_Ankermit_2015_ExVivo_GSE55953_GPL14550 | gamma ray | Homo sapiens | ExVivo | GSE55953 |
| SE_Broustas_2018_InVivo_GSE113509_GPL11202 | Neutron; X-ray | Mus musculus | InVivo | GSE113509 |
| SE_Broustas_2017_InVivo_GSE85323_GPL10333 | Neutron; X-ray | Mus musculus | InVivo | GSE85323 |
| SE_Broustas_2017_ExVivo_GSE90909_GPL13497 | Neutron; X-ray | Homo sapiens | ExVivo | GSE90909 |
| SE_Paul_2010_InVivo_GSE23393_GPL6480 | X-ray | Homo sapiens | InVivo | GSE23393 |
| SE_Ghandhi_2015_ExVivo_GSE65292_GPL13497 | X-ray | Homo sapiens | ExVivo | GSE65292 |
| SE_Flores_2009_ExVivo_GSE15341_GPL8332 | X-ray | Homo sapiens | ExVivo | GSE15341 |
| SE_Amundson_2011_InVivo_GSE20162_GPL6480 | X-ray | Homo sapiens | InVivo | GSE20162 |
| SE_Broustas_2023_InVivo_GSE196400_GPL11202 | X-ray | Mus musculus | InVivo | GSE196400 |
| SE_Broustas_2022_InVivo_GSE184361_GPL11202 | X-ray | Mus musculus | InVivo | GSE184361 |
| SE_Broustas_2021_InVivo_GSE132559_GPL11202 | X-ray | Mus musculus | InVivo | GSE132559 |
| SE_Yamaguchi_2020_InVivo_GSE137192_GPL1261 | X-ray | Mus musculus | InVivo | GSE137192 |
| SE_Mukherjee_2019_InVivo_GSE114142_GPL11202 | X-ray | Mus musculus | InVivo | GSE114142 |
| SE_Amundson_2018_InVivo_GSE101402_GPL11202 | X-ray | Mus musculus | InVivo | GSE101402 |
| SE_Amundson_2018_InVivo_GSE99176_GPL11202 | X-ray | Mus musculus | InVivo | GSE99176 |
| SE_Paul_2015_InVivo_GSE62623_GPL10333 | X-ray | Mus musculus | InVivo | GSE62623 |
| SE_Ghandhi_2018_InVivo_GSE84898_GPL13497 | X-ray | Macaca mulatta | InVivo | GSE84898 |
| SE_Broustas_2021_InVivo_GSE133451_GPL11202 | X-ray | Mus musculus | InVivo | GSE133451 |
| SE_Salah_2025_ExVivo | X-ray | Homo sapiens | ExVivo | NA |
You can use the function get_all_DoReMiTra_datasets() to download all available DoReMiTra datasets from ExperimentHub.
In this example, we fetched all the DoReMiTra datasets which is outputted as a named list from which you can easily access any SE object like (Salah et al. 2025) dataset simply by subsetting.
all_SEs <- get_all_DoReMiTra_datasets()
# Now you can access any loaded dataset by its name, for example:
all_SEs[["SE_Salah_2025_ExVivo"]]With the search_DoReMiTra_datasets() function, you can filter datasets based on radiation type, organism, and experimental setting.
For example, in the following chunk we search for datasets where human samples have been exposed to gamma ray in an ex vivo setting.
search_DoReMiTra_datasets(radiation_type = "gamma ray",
organism = "Homo sapiens",
exp_setting = "ExVivo")
#> Filtering for radiation type: gamma ray
#> Filtering for organism: Homo sapiens
#> Filtering for experimental setting: ExVivo
#>
#> Matching datasets found: 14
#> To retrieve one or more of these datasets, you can use:
#> se_name1 <- get_DoReMiTra_data("SE_Park_2017_ExVivo_GSE102971_GPL10332_HomoSapiens")
#> se_name2 <- get_DoReMiTra_data("SE_Vasilyev_2017_ExVivo_GSE97000_GPL17077")
#>
#> For more details, please refer to `?get_DoReMiTra_data`
#> [1] "SE_Park_2017_ExVivo_GSE102971_GPL10332_HomoSapiens"
#> [2] "SE_Vasilyev_2017_ExVivo_GSE97000_GPL17077"
#> [3] "SE_Paul_2013_ExVivo_GSE44201_GPL6480"
#> [4] "SE_Paul_2013_ExVivo_GSE44201_GPL6848"
#> [5] "SE_Nosel_2013_ExVivo_GSE43151_GPL13497"
#> [6] "SE_Girardi_2012_ExVivo_GSE20173_GPL6480"
#> [7] "SE_Amundson_2011_ExVivo_GSE23515_GPL6480"
#> [8] "SE_Gruel_2008_ExVivo_GSE6978_GPL4803"
#> [9] "SE_Rouchka_2019_ExVivo_GSE63952_GPL15207"
#> [10] "SE_Amundson_2008_ExVivo_GSE8917_GPL1708"
#> [11] "SE_Manikandan_2014_ExVivo_GSE36355_GPL6883"
#> [12] "SE_Lee_2013_ExVivo_GSE44245_GPL570"
#> [13] "SE_Rouchka_2015_ExVivo_GSE64375_GPL6244"
#> [14] "SE_Ankermit_2015_ExVivo_GSE55953_GPL14550"To access an individual dataset, use its exact name as provided by list_DoReMiTra_datasets().
This function contains “gene_symbol” argument that is set to TRUE by default, which assigns the gene symbol from the rowData to the rownames of the SE object. if a gene symbol was found to be duplicated, the gene symbol and its corresponding probe id will be appended and assigned to the rownames. if a gene symbol is messing- NA- the probe id will be used instead. otherwise, if the gene_symbol is set to FALSE, probe ids will be used as rownames
search_DoReMiTra_datasets(radiation_type = "X-ray",
organism = "Homo sapiens",
exp_setting = "ExVivo")
#> Filtering for radiation type: X-ray
#> Filtering for organism: Homo sapiens
#> Filtering for experimental setting: ExVivo
#>
#> Matching datasets found: 4
#> To retrieve one or more of these datasets, you can use:
#> se_name1 <- get_DoReMiTra_data("SE_Broustas_2017_ExVivo_GSE90909_GPL13497")
#> se_name2 <- get_DoReMiTra_data("SE_Ghandhi_2015_ExVivo_GSE65292_GPL13497")
#>
#> For more details, please refer to `?get_DoReMiTra_data`
#> [1] "SE_Broustas_2017_ExVivo_GSE90909_GPL13497"
#> [2] "SE_Ghandhi_2015_ExVivo_GSE65292_GPL13497"
#> [3] "SE_Flores_2009_ExVivo_GSE15341_GPL8332"
#> [4] "SE_Salah_2025_ExVivo"
dataset_name <- "SE_Broustas_2017_ExVivo_GSE90909_GPL13497"
se <- get_DoReMiTra_data(dataset_name, gene_symbol = TRUE)
#> see ?DoReMiTra and browseVignettes('DoReMiTra') for documentation
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
se
#> class: SummarizedExperiment
#> dim: 12289 92
#> metadata(1): DoReMiTra
#> assays(1): exprs
#> rownames(12289): _(+)E1A_r60_1 _(+)E1A_r60_3 ... _ETG10_234183
#> _GE_BrightCorner
#> rowData names(18): ID SPOT_ID ... SEQUENCE SYMBOL
#> colnames(92): GSM2417353 GSM2417354 ... GSM2417443 GSM2417444
#> colData names(44): title geo_accession ... TaxonomyId Exp_settingEach dataset is a SummarizedExperiment object with gene-level expression values, sample-level metadata (colData) and gene annotations (rowData):
assay(se)[1:5, 1:5] # expression matrix
#> GSM2417353 GSM2417354 GSM2417355 GSM2417356 GSM2417357
#> _(+)E1A_r60_1 18.115025 17.673410 17.577608 18.373386 17.952204
#> _(+)E1A_r60_3 3.947578 2.215706 2.473996 2.886919 2.374902
#> _(+)E1A_r60_a104 5.122130 4.716759 3.974693 3.266030 3.144284
#> _(+)E1A_r60_a107 4.961576 4.226226 4.386784 4.988791 4.612860
#> _(+)E1A_r60_a135 7.657646 7.323098 7.118343 7.914989 7.519629
head(rowData(se)) # gene info
#> DataFrame with 6 rows and 18 columns
#> ID SPOT_ID CONTROL_TYPE REFSEQ
#> <character> <character> <character> <character>
#> _(+)E1A_r60_1 (+)E1A_r60_1 (+)E1A_r60_1 pos
#> _(+)E1A_r60_3 (+)E1A_r60_3 (+)E1A_r60_3 pos
#> _(+)E1A_r60_a104 (+)E1A_r60_a104 (+)E1A_r60_a104 pos
#> _(+)E1A_r60_a107 (+)E1A_r60_a107 (+)E1A_r60_a107 pos
#> _(+)E1A_r60_a135 (+)E1A_r60_a135 (+)E1A_r60_a135 pos
#> _(+)E1A_r60_a20 (+)E1A_r60_a20 (+)E1A_r60_a20 pos
#> GB_ACC GENE GENE_SYMBOL GENE_NAME UNIGENE_ID
#> <character> <integer> <character> <character> <character>
#> _(+)E1A_r60_1 NA
#> _(+)E1A_r60_3 NA
#> _(+)E1A_r60_a104 NA
#> _(+)E1A_r60_a107 NA
#> _(+)E1A_r60_a135 NA
#> _(+)E1A_r60_a20 NA
#> ENSEMBL_ID TIGR_ID ACCESSION_STRING CHROMOSOMAL_LOCATION
#> <character> <logical> <character> <character>
#> _(+)E1A_r60_1 NA
#> _(+)E1A_r60_3 NA
#> _(+)E1A_r60_a104 NA
#> _(+)E1A_r60_a107 NA
#> _(+)E1A_r60_a135 NA
#> _(+)E1A_r60_a20 NA
#> CYTOBAND DESCRIPTION GO_ID SEQUENCE SYMBOL
#> <character> <character> <character> <character> <character>
#> _(+)E1A_r60_1
#> _(+)E1A_r60_3
#> _(+)E1A_r60_a104
#> _(+)E1A_r60_a107
#> _(+)E1A_r60_a135
#> _(+)E1A_r60_a20
head(colData(se)) # sample info
#> DataFrame with 6 rows and 44 columns
#> title geo_accession status
#> <character> <character> <character>
#> GSM2417353 blood 0.25Gy Neutron.. GSM2417353 Public on Feb 22 2017
#> GSM2417354 blood 0.5Gy Neutron .. GSM2417354 Public on Feb 22 2017
#> GSM2417355 blood 1Gy Neutron rep1 GSM2417355 Public on Feb 22 2017
#> GSM2417356 blood 1Gy X-ray rep1 GSM2417356 Public on Feb 22 2017
#> GSM2417357 blood 2Gy X-ray rep1 GSM2417357 Public on Feb 22 2017
#> GSM2417358 blood 4Gy X-ray rep1 GSM2417358 Public on Feb 22 2017
#> submission_date last_update_date type channel_count
#> <character> <character> <character> <character>
#> GSM2417353 Dec 05 2016 Feb 24 2017 RNA 1
#> GSM2417354 Dec 05 2016 Feb 24 2017 RNA 1
#> GSM2417355 Dec 05 2016 Feb 24 2017 RNA 1
#> GSM2417356 Dec 05 2016 Feb 24 2017 RNA 1
#> GSM2417357 Dec 05 2016 Feb 24 2017 RNA 1
#> GSM2417358 Dec 05 2016 Feb 24 2017 RNA 1
#> source_name_ch1 organism_ch1 characteristics_ch1
#> <character> <character> <character>
#> GSM2417353 blood 0.25Gy Neutron Homo sapiens donor: Donor 1
#> GSM2417354 blood 0.5Gy Neutron Homo sapiens donor: Donor 1
#> GSM2417355 blood 1Gy Neutron Homo sapiens donor: Donor 1
#> GSM2417356 blood 1Gy X-ray Homo sapiens donor: Donor 1
#> GSM2417357 blood 2Gy X-ray Homo sapiens donor: Donor 1
#> GSM2417358 blood 4Gy X-ray Homo sapiens donor: Donor 1
#> characteristics_ch1.1 treatment_protocol_ch1 growth_protocol_ch1
#> <character> <character> <character>
#> GSM2417353 tissue: peripheral b.. Peripheral blood fro.. After irradiation, b..
#> GSM2417354 tissue: peripheral b.. Peripheral blood fro.. After irradiation, b..
#> GSM2417355 tissue: peripheral b.. Peripheral blood fro.. After irradiation, b..
#> GSM2417356 tissue: peripheral b.. Peripheral blood fro.. After irradiation, b..
#> GSM2417357 tissue: peripheral b.. Peripheral blood fro.. After irradiation, b..
#> GSM2417358 tissue: peripheral b.. Peripheral blood fro.. After irradiation, b..
#> molecule_ch1 extract_protocol_ch1 label_ch1
#> <character> <character> <character>
#> GSM2417353 total RNA The RNA was prepared.. Cy3
#> GSM2417354 total RNA The RNA was prepared.. Cy3
#> GSM2417355 total RNA The RNA was prepared.. Cy3
#> GSM2417356 total RNA The RNA was prepared.. Cy3
#> GSM2417357 total RNA The RNA was prepared.. Cy3
#> GSM2417358 total RNA The RNA was prepared.. Cy3
#> label_protocol_ch1 taxid_ch1 hyb_protocol
#> <character> <character> <character>
#> GSM2417353 Cyanine-3 (Cy3) labe.. 9606 1.65 ug of Cy3-label..
#> GSM2417354 Cyanine-3 (Cy3) labe.. 9606 1.65 ug of Cy3-label..
#> GSM2417355 Cyanine-3 (Cy3) labe.. 9606 1.65 ug of Cy3-label..
#> GSM2417356 Cyanine-3 (Cy3) labe.. 9606 1.65 ug of Cy3-label..
#> GSM2417357 Cyanine-3 (Cy3) labe.. 9606 1.65 ug of Cy3-label..
#> GSM2417358 Cyanine-3 (Cy3) labe.. 9606 1.65 ug of Cy3-label..
#> scan_protocol data_processing platform_id
#> <character> <character> <character>
#> GSM2417353 Slides were scanned .. The scanned images w.. GPL13497
#> GSM2417354 Slides were scanned .. The scanned images w.. GPL13497
#> GSM2417355 Slides were scanned .. The scanned images w.. GPL13497
#> GSM2417356 Slides were scanned .. The scanned images w.. GPL13497
#> GSM2417357 Slides were scanned .. The scanned images w.. GPL13497
#> GSM2417358 Slides were scanned .. The scanned images w.. GPL13497
#> contact_name contact_email contact_department
#> <character> <character> <character>
#> GSM2417353 Sally,,Amundson saa2108@cumc.columbi.. Center for Radiologi..
#> GSM2417354 Sally,,Amundson saa2108@cumc.columbi.. Center for Radiologi..
#> GSM2417355 Sally,,Amundson saa2108@cumc.columbi.. Center for Radiologi..
#> GSM2417356 Sally,,Amundson saa2108@cumc.columbi.. Center for Radiologi..
#> GSM2417357 Sally,,Amundson saa2108@cumc.columbi.. Center for Radiologi..
#> GSM2417358 Sally,,Amundson saa2108@cumc.columbi.. Center for Radiologi..
#> contact_institute contact_address contact_city contact_state
#> <character> <character> <character> <character>
#> GSM2417353 Columbia University 630 W. 168th St New York NY
#> GSM2417354 Columbia University 630 W. 168th St New York NY
#> GSM2417355 Columbia University 630 W. 168th St New York NY
#> GSM2417356 Columbia University 630 W. 168th St New York NY
#> GSM2417357 Columbia University 630 W. 168th St New York NY
#> GSM2417358 Columbia University 630 W. 168th St New York NY
#> contact_zip.postal_code contact_country supplementary_file
#> <character> <character> <character>
#> GSM2417353 10032 USA ftp://ftp.ncbi.nlm.n..
#> GSM2417354 10032 USA ftp://ftp.ncbi.nlm.n..
#> GSM2417355 10032 USA ftp://ftp.ncbi.nlm.n..
#> GSM2417356 10032 USA ftp://ftp.ncbi.nlm.n..
#> GSM2417357 10032 USA ftp://ftp.ncbi.nlm.n..
#> GSM2417358 10032 USA ftp://ftp.ncbi.nlm.n..
#> data_row_count donor.ch1 tissue.ch1 Dose Time_point
#> <character> <character> <character> <character> <character>
#> GSM2417353 12289 Donor 1 peripheral blood 0.25Gy 24h
#> GSM2417354 12289 Donor 1 peripheral blood 0.5Gy 24h
#> GSM2417355 12289 Donor 1 peripheral blood 1Gy 24h
#> GSM2417356 12289 Donor 1 peripheral blood 1Gy 24h
#> GSM2417357 12289 Donor 1 peripheral blood 2Gy 24h
#> GSM2417358 12289 Donor 1 peripheral blood 4Gy 24h
#> Sex Radiation_type Sample_id Organism Platform
#> <character> <character> <character> <character> <character>
#> GSM2417353 NA Neutron GSM2417353 Homo sapiens Microarray
#> GSM2417354 NA Neutron GSM2417354 Homo sapiens Microarray
#> GSM2417355 NA Neutron GSM2417355 Homo sapiens Microarray
#> GSM2417356 NA X-ray GSM2417356 Homo sapiens Microarray
#> GSM2417357 NA X-ray GSM2417357 Homo sapiens Microarray
#> GSM2417358 NA X-ray GSM2417358 Homo sapiens Microarray
#> TaxonomyId Exp_setting
#> <character> <character>
#> GSM2417353 9606 ExVivo
#> GSM2417354 9606 ExVivo
#> GSM2417355 9606 ExVivo
#> GSM2417356 9606 ExVivo
#> GSM2417357 9606 ExVivo
#> GSM2417358 9606 ExVivoYou can get a quick metadata summary of a dataset using summarize_DoReMiTra_se()which will output key information like the author of the study, number of the samples, organism, experiment setting, and radiation type and dose, and a link directing you to the the study
summarize_DoReMiTra_se(se)
#> This dataset is generated by: Broustas
#> Platform: Microarray
#> Organism(s): Homo sapiens
#> Radiation Type: Neutron; X-ray
#> Experiment Setting: ExVivo
#> Number of Samples: 92
#> Accession: GSE90909
#> For more information about this study, please check:
#> https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90909This is useful for checking compatibility before combined analysis - for example, we first searched for studies that involved gamma ray irradiation of homo sapiens samples. from the number of studies that are shown, we want to compare between (Park et al. 2017) and (Paul and Amundson 2008)
search_DoReMiTra_datasets(radiation_type = "gamma ray",
organism = "Homo sapiens",
exp_setting = "ExVivo")
#> Filtering for radiation type: gamma ray
#> Filtering for organism: Homo sapiens
#> Filtering for experimental setting: ExVivo
#>
#> Matching datasets found: 14
#> To retrieve one or more of these datasets, you can use:
#> se_name1 <- get_DoReMiTra_data("SE_Park_2017_ExVivo_GSE102971_GPL10332_HomoSapiens")
#> se_name2 <- get_DoReMiTra_data("SE_Vasilyev_2017_ExVivo_GSE97000_GPL17077")
#>
#> For more details, please refer to `?get_DoReMiTra_data`
#> [1] "SE_Park_2017_ExVivo_GSE102971_GPL10332_HomoSapiens"
#> [2] "SE_Vasilyev_2017_ExVivo_GSE97000_GPL17077"
#> [3] "SE_Paul_2013_ExVivo_GSE44201_GPL6480"
#> [4] "SE_Paul_2013_ExVivo_GSE44201_GPL6848"
#> [5] "SE_Nosel_2013_ExVivo_GSE43151_GPL13497"
#> [6] "SE_Girardi_2012_ExVivo_GSE20173_GPL6480"
#> [7] "SE_Amundson_2011_ExVivo_GSE23515_GPL6480"
#> [8] "SE_Gruel_2008_ExVivo_GSE6978_GPL4803"
#> [9] "SE_Rouchka_2019_ExVivo_GSE63952_GPL15207"
#> [10] "SE_Amundson_2008_ExVivo_GSE8917_GPL1708"
#> [11] "SE_Manikandan_2014_ExVivo_GSE36355_GPL6883"
#> [12] "SE_Lee_2013_ExVivo_GSE44245_GPL570"
#> [13] "SE_Rouchka_2015_ExVivo_GSE64375_GPL6244"
#> [14] "SE_Ankermit_2015_ExVivo_GSE55953_GPL14550"
se1 <- get_DoReMiTra_data("SE_Park_2017_ExVivo_GSE102971_GPL10332_HomoSapiens")
#> see ?DoReMiTra and browseVignettes('DoReMiTra') for documentation
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
se2 <- get_DoReMiTra_data("SE_Paul_2013_ExVivo_GSE44201_GPL6480")
#> see ?DoReMiTra and browseVignettes('DoReMiTra') for documentation
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
se_list<- list(
Park = se1,
Paul = se2
)
compare_DoReMiTra_datasets(se_list = se_list)
#> Park Paul
#> Radiation_type gamma ray gamma ray
#> Dose 0Gy, 2Gy, 5Gy, 6Gy, 7Gy 0.5Gy, 0Gy, 2Gy, 5Gy, 8Gy
#> Sex Female, Male female, male
#> Time_point 24h 48hr
#> Organism Homo sapiens Homo sapiens
#> Sample_number 100 25list_DoReMiTra_datasets() when calling get_DoReMiTra_data().search_DoReMiTra_datasets() to dynamically find datasets of interest based on key metadata fields.To cite the datasets or studies, please refer to the original GEO accession IDs (e.g., GSE124612). More details are included in the metadata, which you can easily access via summarize_DoReMiTra_se().
sessionInfo()
#> R version 4.5.1 Patched (2025-08-23 r88802)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.3 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_GB LC_COLLATE=C
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: America/New_York
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] DoReMiTra_0.99.2 ExperimentHub_2.99.5
#> [3] AnnotationHub_3.99.6 BiocFileCache_2.99.6
#> [5] dbplyr_2.5.1 SummarizedExperiment_1.39.2
#> [7] Biobase_2.69.1 GenomicRanges_1.61.5
#> [9] Seqinfo_0.99.2 IRanges_2.43.5
#> [11] S4Vectors_0.47.4 BiocGenerics_0.55.4
#> [13] generics_0.1.4 MatrixGenerics_1.21.0
#> [15] matrixStats_1.5.0 BiocStyle_2.37.1
#>
#> loaded via a namespace (and not attached):
#> [1] tidyselect_1.2.1 viridisLite_0.4.2
#> [3] vipor_0.4.7 dplyr_1.1.4
#> [5] farver_2.1.2 blob_1.2.4
#> [7] viridis_0.6.5 S7_0.2.0
#> [9] filelock_1.0.3 Biostrings_2.77.2
#> [11] fastmap_1.2.0 SingleCellExperiment_1.31.1
#> [13] digest_0.6.37 rsvd_1.0.5
#> [15] lifecycle_1.0.4 KEGGREST_1.49.2
#> [17] RSQLite_2.4.3 magrittr_2.0.4
#> [19] compiler_4.5.1 rlang_1.1.6
#> [21] sass_0.4.10 tools_4.5.1
#> [23] yaml_2.3.10 knitr_1.50
#> [25] S4Arrays_1.9.1 bit_4.6.0
#> [27] curl_7.0.0 DelayedArray_0.35.3
#> [29] RColorBrewer_1.1-3 abind_1.4-8
#> [31] BiocParallel_1.43.4 withr_3.0.2
#> [33] purrr_1.1.0 grid_4.5.1
#> [35] beachmat_2.25.5 ggplot2_4.0.0
#> [37] scales_1.4.0 dichromat_2.0-0.1
#> [39] cli_3.6.5 rmarkdown_2.30
#> [41] crayon_1.5.3 httr_1.4.7
#> [43] DBI_1.2.3 scuttle_1.19.0
#> [45] ggbeeswarm_0.7.2 cachem_1.1.0
#> [47] parallel_4.5.1 AnnotationDbi_1.71.2
#> [49] BiocManager_1.30.26 XVector_0.49.1
#> [51] vctrs_0.6.5 Matrix_1.7-4
#> [53] jsonlite_2.0.0 bookdown_0.45
#> [55] BiocSingular_1.25.0 BiocNeighbors_2.3.1
#> [57] ggrepel_0.9.6 bit64_4.6.0-1
#> [59] beeswarm_0.4.0 irlba_2.3.5.1
#> [61] scater_1.37.0 jquerylib_0.1.4
#> [63] glue_1.8.0 codetools_0.2-20
#> [65] gtable_0.3.6 BiocVersion_3.22.0
#> [67] ScaledMatrix_1.17.0 tibble_3.3.0
#> [69] pillar_1.11.1 rappdirs_0.3.3
#> [71] htmltools_0.5.8.1 R6_2.6.1
#> [73] httr2_1.2.1 evaluate_1.0.5
#> [75] lattice_0.22-7 png_0.1-8
#> [77] memoise_2.0.1 bslib_0.9.0
#> [79] Rcpp_1.1.0 gridExtra_2.3
#> [81] SparseArray_1.9.1 xfun_0.53
#> [83] pkgconfig_2.0.3Park, Jin G., Sunirmal Paul, Natalia Briones, Jia Zeng, Kristin Gillis, Garrick Wallstrom, Joshua LaBaer, and Sally A. Amundson. 2017. “Developing Human Radiation Biodosimetry Models: Testing Cross-Species Conversion Approaches Using an Ex Vivo Model System.” Radiation Research 187 (6): 708. https://doi.org/10.1667/rr14655.1.
Paul, Sunirmal, and Sally A. Amundson. 2008. “Development of Gene Expression Signatures for Practical Radiation Biodosimetry.” International Journal of Radiation Oncology*Biology*Physics 71 (4): 1236–1244.e76. https://doi.org/10.1016/j.ijrobp.2008.03.043.
Salah, Ahmed, Daniel Wollschläger, Maurizio Callari, Heinz Schmidberger, Federico Marini, and Sebastian Zahnreich. 2025. “Genome-Wide Transcriptomic Response of Whole Blood to Radiation.” Scientific Reports 15 (1). https://doi.org/10.1038/s41598-025-04898-1.