Getting Started • refinebioc

Introduction

The refinebioc package is a collection of functions that can be used to refine Bioconductor objects. The package is designed to be used in conjunction with the BiocFileCache package, which provides a way to cache Bioconductor objects on disk. The refinebioc package provides functions to refine these cached objects, such as filtering, normalizing, and transforming data.

Installation

You can install the refinebioc package from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install("seandavi/refinebioc")

Usage

Loading the package

library(refinebioc)
rb_set_email_address("seandavi@gmail.com")

Experiments

The experiment_listing function can be used to list all available experiments.

experiments <- get_experiment_catalog()

To get a feel for the data, we can look at the first few rows of the data frame.

head(experiments)
#> # A tibble: 6 × 21
#>      id title            publication_title description technology accession_code
#>   <int> <chr>            <chr>             <chr>       <chr>      <chr>         
#> 1 52090 Shared and dist… Shared and disti… Neocortex … RNA-SEQ    SRP150473     
#> 2 51049 Transcriptome a… Conserved proper… RNA sequen… RNA-SEQ    SRP118985     
#> 3 47744 In vivo molecul… Broadly neutrali… Dengue vir… RNA-SEQ    SRP152576     
#> 4 67685 Drug-induced ch… The NCI Transcri… To identif… MICROARRAY GSE116436     
#> 5 50699 Single-cell tra… Classes and cont… We  studie… RNA-SEQ    SRP109000     
#> 6 51542 Single cell RNA… Diversity of Int… In order t… RNA-SEQ    SRP124669     
#> # ℹ 15 more variables: alternate_accession_code <chr>,
#> #   submitter_institution <chr>, has_publication <lgl>, publication_doi <chr>,
#> #   publication_authors <list>, sample_metadata_fields <list>,
#> #   platform_names <list>, platform_accession_codes <list>,
#> #   organism_names <list>, downloadable_organism_names <list>, pubmed_id <chr>,
#> #   num_total_samples <int>, num_processed_samples <int>,
#> #   num_downloadable_samples <int>, source_first_published <date>

The experiments variable contains a data frame. Standard dplyr functions can be used to filter and sort the data frame.

library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
experiments %>%
    dplyr::filter(grepl("GSE1133", accession_code)) %>%
    dplyr::select(accession_code, title)
#> # A tibble: 1 × 2
#>   accession_code title                                     
#>   <chr>          <chr>                                     
#> 1 GSE1133        tissue-specific pattern of mRNA expression

Loading an experiment

The rb_get_experiment function loads the experiment data into memory. The refine.bio website and API, from which the data is loaded, prepares the data asynchronously, so this function will wait until the data is ready, often taking a few minutes. Do not interrupt the function while it is running.

# Load the GSE1133 experiment
expts <- get_refinebio("GSE1133")
#> INFO [2025-03-04 23:34:38] Registered dataset request: 9d1a2fe1-b176-4661-bdd1-9f49b5d35eec
#> INFO [2025-03-04 23:34:38] Starting to process at RefineBio:  9d1a2fe1-b176-4661-bdd1-9f49b5d35eec
#> INFO [2025-03-04 23:34:38] This may take many minutes, depending on data size.
#> INFO [2025-03-04 23:34:38] Wait for RefineBio to process:  9d1a2fe1-b176-4661-bdd1-9f49b5d35eec
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#> INFO [2025-03-05 04:56:15] RefineBio finished processing:  9d1a2fe1-b176-4661-bdd1-9f49b5d35eec
#> INFO [2025-03-05 04:56:15] Dataset available:  9d1a2fe1-b176-4661-bdd1-9f49b5d35eec
#> INFO [2025-03-05 04:56:15] Starting to download:  9d1a2fe1-b176-4661-bdd1-9f49b5d35eec
#> 
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#> INFO [2025-03-05 04:56:15] Dataset downloaded:  9d1a2fe1-b176-4661-bdd1-9f49b5d35eec
#> INFO [2025-03-05 04:56:15] Starting to extract:  9d1a2fe1-b176-4661-bdd1-9f49b5d35eec
#> INFO [2025-03-05 04:56:15] Dataset extracted:  9d1a2fe1-b176-4661-bdd1-9f49b5d35eec
#> INFO [2025-03-05 04:56:20] Dataset loaded:  9d1a2fe1-b176-4661-bdd1-9f49b5d35eec

The expts variable contains a list of SummarizedExperiment objects.

expts$GSE1133
#> class: SummarizedExperiment 
#> dim: 11868 158 
#> metadata(13): accession_code description ... technology title
#> assays(1): exprs
#> rownames: NULL
#> rowData names(1): Gene
#> colnames(158): GSM18865 GSM18866 ... GSM19021 GSM19022
#> colData names(57): refinebio_accession_code experiment_accession ...
#>   title type

To view the sample information, use the colData function.

SummarizedExperiment::colData(expts$GSE1133)
#> DataFrame with 158 rows and 57 columns
#>          refinebio_accession_code experiment_accession refinebio_age
#>                       <character>          <character>     <logical>
#> GSM18865                 GSM18865              GSE1133            NA
#> GSM18866                 GSM18866              GSE1133            NA
#> GSM18867                 GSM18867              GSE1133            NA
#> GSM18868                 GSM18868              GSE1133            NA
#> GSM18869                 GSM18869              GSE1133            NA
#> ...                           ...                  ...           ...
#> GSM19018                 GSM19018              GSE1133            NA
#> GSM19019                 GSM19019              GSE1133            NA
#> GSM19020                 GSM19020              GSE1133            NA
#> GSM19021                 GSM19021              GSE1133            NA
#> GSM19022                 GSM19022              GSE1133            NA
#>          refinebio_cell_line refinebio_compound refinebio_developmental_stage
#>                    <logical>          <logical>                     <logical>
#> GSM18865                  NA                 NA                            NA
#> GSM18866                  NA                 NA                            NA
#> GSM18867                  NA                 NA                            NA
#> GSM18868                  NA                 NA                            NA
#> GSM18869                  NA                 NA                            NA
#> ...                      ...                ...                           ...
#> GSM19018                  NA                 NA                            NA
#> GSM19019                  NA                 NA                            NA
#> GSM19020                  NA                 NA                            NA
#> GSM19021                  NA                 NA                            NA
#> GSM19022                  NA                 NA                            NA
#>          refinebio_disease refinebio_disease_stage
#>                  <logical>               <logical>
#> GSM18865                NA                      NA
#> GSM18866                NA                      NA
#> GSM18867                NA                      NA
#> GSM18868                NA                      NA
#> GSM18869                NA                      NA
#> ...                    ...                     ...
#> GSM19018                NA                      NA
#> GSM19019                NA                      NA
#> GSM19020                NA                      NA
#> GSM19021                NA                      NA
#> GSM19022                NA                      NA
#>          refinebio_genetic_information refinebio_organism
#>                              <logical>        <character>
#> GSM18865                            NA       HOMO_SAPIENS
#> GSM18866                            NA       HOMO_SAPIENS
#> GSM18867                            NA       HOMO_SAPIENS
#> GSM18868                            NA       HOMO_SAPIENS
#> GSM18869                            NA       HOMO_SAPIENS
#> ...                                ...                ...
#> GSM19018                            NA       HOMO_SAPIENS
#> GSM19019                            NA       HOMO_SAPIENS
#> GSM19020                            NA       HOMO_SAPIENS
#> GSM19021                            NA       HOMO_SAPIENS
#> GSM19022                            NA       HOMO_SAPIENS
#>              refinebio_platform refinebio_processed refinebio_processor_id
#>                     <character>           <logical>              <integer>
#> GSM18865 Affymetrix Human Gen..                TRUE                    483
#> GSM18866 Affymetrix Human Gen..                TRUE                    483
#> GSM18867 Affymetrix Human Gen..                TRUE                    483
#> GSM18868 Affymetrix Human Gen..                TRUE                    483
#> GSM18869 Affymetrix Human Gen..                TRUE                    483
#> ...                         ...                 ...                    ...
#> GSM19018 Affymetrix Human Gen..                TRUE                    483
#> GSM19019 Affymetrix Human Gen..                TRUE                    483
#> GSM19020 Affymetrix Human Gen..                TRUE                    483
#> GSM19021 Affymetrix Human Gen..                TRUE                    483
#> GSM19022 Affymetrix Human Gen..                TRUE                    483
#>          refinebio_processor_name refinebio_processor_version refinebio_race
#>                       <character>                 <character>      <logical>
#> GSM18865          Affymetrix SCAN             v1.27.32-hotfix             NA
#> GSM18866          Affymetrix SCAN             v1.27.32-hotfix             NA
#> GSM18867          Affymetrix SCAN             v1.27.32-hotfix             NA
#> GSM18868          Affymetrix SCAN             v1.27.32-hotfix             NA
#> GSM18869          Affymetrix SCAN             v1.27.32-hotfix             NA
#> ...                           ...                         ...            ...
#> GSM19018          Affymetrix SCAN             v1.27.32-hotfix             NA
#> GSM19019          Affymetrix SCAN             v1.27.32-hotfix             NA
#> GSM19020          Affymetrix SCAN             v1.27.32-hotfix             NA
#> GSM19021          Affymetrix SCAN             v1.27.32-hotfix             NA
#> GSM19022          Affymetrix SCAN             v1.27.32-hotfix             NA
#>          refinebio_sex refinebio_source_archive_url refinebio_source_database
#>              <logical>                    <logical>               <character>
#> GSM18865            NA                           NA                       GEO
#> GSM18866            NA                           NA                       GEO
#> GSM18867            NA                           NA                       GEO
#> GSM18868            NA                           NA                       GEO
#> GSM18869            NA                           NA                       GEO
#> ...                ...                          ...                       ...
#> GSM19018            NA                           NA                       GEO
#> GSM19019            NA                           NA                       GEO
#> GSM19020            NA                           NA                       GEO
#> GSM19021            NA                           NA                       GEO
#> GSM19022            NA                           NA                       GEO
#>          refinebio_specimen_part refinebio_subject refinebio_time
#>                        <logical>         <logical>      <logical>
#> GSM18865                      NA                NA             NA
#> GSM18866                      NA                NA             NA
#> GSM18867                      NA                NA             NA
#> GSM18868                      NA                NA             NA
#> GSM18869                      NA                NA             NA
#> ...                          ...               ...            ...
#> GSM19018                      NA                NA             NA
#> GSM19019                      NA                NA             NA
#> GSM19020                      NA                NA             NA
#> GSM19021                      NA                NA             NA
#> GSM19022                      NA                NA             NA
#>                 refinebio_title refinebio_treatment channel_count
#>                     <character>           <logical>     <integer>
#> GSM18865 3AMH02022201_Colorec..                  NA             1
#> GSM18866 3AMH02030601_Colorec..                  NA             1
#> GSM18867 3AJZ02052318_WHOLEBL..                  NA             1
#> GSM18868 3AJZ02052320_WHOLEBL..                  NA             1
#> GSM18869 3AMH02082105_BM_CD33..                  NA             1
#> ...                         ...                 ...           ...
#> GSM19018   3AJZ02082987B_TONGUE                  NA             1
#> GSM19019 3AJZ02060514_Olfacto..                  NA             1
#> GSM19020 3AJZ02072561_Olfacto..                  NA             1
#> GSM19021 3AJZ02022867_Pituitary                  NA             1
#> GSM19022 3AJZ02030476_pituitary                  NA             1
#>                 contact_address contact_city contact_country   contact_email
#>                     <character>  <character>     <character>     <character>
#> GSM18865 10675 John Jay Hopkins    San Diego             USA jwalker@gnf.org
#> GSM18866 10675 John Jay Hopkins    San Diego             USA jwalker@gnf.org
#> GSM18867 10675 John Jay Hopkins    San Diego             USA jwalker@gnf.org
#> GSM18868 10675 John Jay Hopkins    San Diego             USA jwalker@gnf.org
#> GSM18869 10675 John Jay Hopkins    San Diego             USA jwalker@gnf.org
#> ...                         ...          ...             ...             ...
#> GSM19018 10675 John Jay Hopkins    San Diego             USA jwalker@gnf.org
#> GSM19019 10675 John Jay Hopkins    San Diego             USA jwalker@gnf.org
#> GSM19020 10675 John Jay Hopkins    San Diego             USA jwalker@gnf.org
#> GSM19021 10675 John Jay Hopkins    San Diego             USA jwalker@gnf.org
#> GSM19022 10675 John Jay Hopkins    San Diego             USA jwalker@gnf.org
#>               contact_institute contact_laboratory  contact_name contact_phone
#>                     <character>        <character>   <character>   <character>
#> GSM18865 Genomics Institute o..      Genetics Core John,R,Walker  858-812-1636
#> GSM18866 Genomics Institute o..      Genetics Core John,R,Walker  858-812-1636
#> GSM18867 Genomics Institute o..      Genetics Core John,R,Walker  858-812-1636
#> GSM18868 Genomics Institute o..      Genetics Core John,R,Walker  858-812-1636
#> GSM18869 Genomics Institute o..      Genetics Core John,R,Walker  858-812-1636
#> ...                         ...                ...           ...           ...
#> GSM19018 Genomics Institute o..      Genetics Core John,R,Walker  858-812-1636
#> GSM19019 Genomics Institute o..      Genetics Core John,R,Walker  858-812-1636
#> GSM19020 Genomics Institute o..      Genetics Core John,R,Walker  858-812-1636
#> GSM19021 Genomics Institute o..      Genetics Core John,R,Walker  858-812-1636
#> GSM19022 Genomics Institute o..      Genetics Core John,R,Walker  858-812-1636
#>          contact_state contact_zip/postal_code data_processing data_row_count
#>            <character>               <integer>     <character>      <integer>
#> GSM18865            CA                   92121            MAS5          22283
#> GSM18866            CA                   92121            MAS5          22283
#> GSM18867            CA                   92121            MAS5          22283
#> GSM18868            CA                   92121            MAS5          22283
#> GSM18869            CA                   92121            MAS5          22283
#> ...                ...                     ...             ...            ...
#> GSM19018            CA                   92121            MAS5          22283
#> GSM19019            CA                   92121            MAS5          22283
#> GSM19020            CA                   92121            MAS5          22283
#> GSM19021            CA                   92121            MAS5          22283
#> GSM19022            CA                   92121            MAS5          22283
#>                     description   extract_protocol_ch1 geo_accession
#>                     <character>            <character>   <character>
#> GSM18865   Colorectal Adenocarc Human tissue samples..      GSM18865
#> GSM18866 Colorectal Adenocarc.. Human tissue samples..      GSM18866
#> GSM18867             WHOLEBLOOD Human tissue samples..      GSM18867
#> GSM18868             WHOLEBLOOD Human tissue samples..      GSM18868
#> GSM18869 bone marrow-CD33Myel.. Human tissue samples..      GSM18869
#> ...                         ...                    ...           ...
#> GSM19018                 TONGUE Human tissue samples..      GSM19018
#> GSM19019          OlfactoryBulb Human tissue samples..      GSM19019
#> GSM19020          OlfactoryBulb Human tissue samples..      GSM19020
#> GSM19021              Pituitary Human tissue samples..      GSM19021
#> GSM19022              pituitary Human tissue samples..      GSM19022
#>                    hyb_protocol   label_ch1     label_protocol_ch1
#>                     <character> <character>            <character>
#> GSM18865 standard Affymetrix ..      biotin Five micrograms of t..
#> GSM18866 standard Affymetrix ..      biotin Five micrograms of t..
#> GSM18867 standard Affymetrix ..      biotin Five micrograms of t..
#> GSM18868 standard Affymetrix ..      biotin Five micrograms of t..
#> GSM18869 standard Affymetrix ..      biotin Five micrograms of t..
#> ...                         ...         ...                    ...
#> GSM19018 standard Affymetrix ..      biotin Five micrograms of t..
#> GSM19019 standard Affymetrix ..      biotin Five micrograms of t..
#> GSM19020 standard Affymetrix ..      biotin Five micrograms of t..
#> GSM19021 standard Affymetrix ..      biotin Five micrograms of t..
#> GSM19022 standard Affymetrix ..      biotin Five micrograms of t..
#>          last_update_date molecule_ch1 organism_ch1 platform_id    relation
#>               <character>  <character>  <character> <character> <character>
#> GSM18865      Sep 25 2006    total RNA Homo sapiens       GPL96            
#> GSM18866      Sep 25 2006    total RNA Homo sapiens       GPL96            
#> GSM18867      Sep 25 2006    total RNA Homo sapiens       GPL96            
#> GSM18868      Sep 25 2006    total RNA Homo sapiens       GPL96            
#> GSM18869      Sep 25 2006    total RNA Homo sapiens       GPL96            
#> ...                   ...          ...          ...         ...         ...
#> GSM19018      Sep 25 2006    total RNA Homo sapiens       GPL96            
#> GSM19019      Sep 25 2006    total RNA Homo sapiens       GPL96            
#> GSM19020      Sep 25 2006    total RNA Homo sapiens       GPL96            
#> GSM19021      Sep 25 2006    total RNA Homo sapiens       GPL96            
#> GSM19022      Sep 25 2006    total RNA Homo sapiens       GPL96            
#>                   scan_protocol   series_id        source_name_ch1
#>                     <character> <character>            <character>
#> GSM18865 standard Affymetrix ..     GSE1133 3AMH02022201_Colorec..
#> GSM18866 standard Affymetrix ..     GSE1133 3AMH02030601_Colorec..
#> GSM18867 standard Affymetrix ..     GSE1133 3AJZ02052318_WHOLEBL..
#> GSM18868 standard Affymetrix ..     GSE1133 3AJZ02052320_WHOLEBL..
#> GSM18869 standard Affymetrix ..     GSE1133 3AMH02082105_BM_CD33..
#> ...                         ...         ...                    ...
#> GSM19018 standard Affymetrix ..     GSE1133   3AJZ02082987B_TONGUE
#> GSM19019 standard Affymetrix ..     GSE1133 3AJZ02060514_Olfacto..
#> GSM19020 standard Affymetrix ..     GSE1133 3AJZ02072561_Olfacto..
#> GSM19021 standard Affymetrix ..     GSE1133 3AJZ02022867_Pituitary
#> GSM19022 standard Affymetrix ..     GSE1133 3AJZ02030476_pituitary
#>                         status submission_date     supplementary_file taxid_ch1
#>                    <character>     <character>            <character> <integer>
#> GSM18865 Public on Mar 19 2004     Mar 18 2004 ftp://ftp.ncbi.nlm.n..      9606
#> GSM18866 Public on Mar 19 2004     Mar 18 2004 ftp://ftp.ncbi.nlm.n..      9606
#> GSM18867 Public on Mar 19 2004     Mar 18 2004 ftp://ftp.ncbi.nlm.n..      9606
#> GSM18868 Public on Mar 19 2004     Mar 18 2004 ftp://ftp.ncbi.nlm.n..      9606
#> GSM18869 Public on Mar 19 2004     Mar 18 2004 ftp://ftp.ncbi.nlm.n..      9606
#> ...                        ...             ...                    ...       ...
#> GSM19018 Public on Mar 19 2004     Mar 18 2004 ftp://ftp.ncbi.nlm.n..      9606
#> GSM19019 Public on Mar 19 2004     Mar 18 2004 ftp://ftp.ncbi.nlm.n..      9606
#> GSM19020 Public on Mar 19 2004     Mar 18 2004 ftp://ftp.ncbi.nlm.n..      9606
#> GSM19021 Public on Mar 19 2004     Mar 18 2004 ftp://ftp.ncbi.nlm.n..      9606
#> GSM19022 Public on Mar 19 2004     Mar 18 2004 ftp://ftp.ncbi.nlm.n..      9606
#>                           title        type
#>                     <character> <character>
#> GSM18865 3AMH02022201_Colorec..         RNA
#> GSM18866 3AMH02030601_Colorec..         RNA
#> GSM18867 3AJZ02052318_WHOLEBL..         RNA
#> GSM18868 3AJZ02052320_WHOLEBL..         RNA
#> GSM18869 3AMH02082105_BM_CD33..         RNA
#> ...                         ...         ...
#> GSM19018   3AJZ02082987B_TONGUE         RNA
#> GSM19019 3AJZ02060514_Olfacto..         RNA
#> GSM19020 3AJZ02072561_Olfacto..         RNA
#> GSM19021 3AJZ02022867_Pituitary         RNA
#> GSM19022 3AJZ02030476_pituitary         RNA