Produces the bibliography list of your workflow

Source: R/get_bibliography.R

get_bibliography() takes as input a `tidybulk`

get_bibliography(.data)

# S4 method for class 'SummarizedExperiment'
get_bibliography(.data)

# S4 method for class 'RangedSummarizedExperiment'
get_bibliography(.data)

Arguments

.data

A `tbl` (with at least three columns for sample, feature and transcript abundance) or `SummarizedExperiment` (more convenient if abstracted to tibble with library(tidySummarizedExperiment))

Value

NULL. It prints a list of bibliography references for the software used through the workflow.

A consistent object (to the input) with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

A consistent object (to the input) with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

Details

`r lifecycle::badge("maturing")`

This methods returns the bibliography list of your workflow from the metadata of a tidybulk object (metadata(.)$tidybulk$methods_used) or from the internals for backward compatibility (attr(., "internals"))

References

Mangiola, S., Molania, R., Dong, R., Doyle, M. A., & Papenfuss, A. T. (2021). tidybulk: an R tidy framework for modular transcriptomic data analysis. Genome Biology, 22(1), 42. doi:10.1186/s13059-020-02233-7

Examples

## Load airway dataset for examples

  data('airway', package = 'airway')
  # Ensure a 'condition' column exists for examples expecting it

    SummarizedExperiment::colData(airway)$condition <- SummarizedExperiment::colData(airway)$dex




get_bibliography(airway)
#>  @Article{tidybulk,
#>   title = {tidybulk: an R tidy framework for modular transcriptomic data analysis},
#>   author = {Stefano Mangiola and Ramyar Molania and Ruining Dong and Maria A. Doyle & Anthony T. Papenfuss},
#>   journal = {Genome Biology},
#>   year = {2021},
#>   volume = {22},
#>   number = {42},
#>   url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02233-7},
#>   }
#> @article{wickham2019welcome,
#>   title={Welcome to the Tidyverse},
#>   author={Wickham, Hadley and Averick, Mara and Bryan, Jennifer and Chang, Winston and McGowan, Lucy D'Agostino and Francois, Romain and Grolemund, Garrett and Hayes, Alex and Henry, Lionel and Hester, Jim and others},
#>   journal={Journal of Open Source Software},
#>   volume={4},
#>   number={43},
#>   pages={1686},
#>   year={2019}
#> 	}