GitHub - multimeric/TidyMultiqc: Converts 'MultiQC' Reports into Tidy Data Frames (original) (raw)

TidyMultiqc

TidyMultiqc Provides the means to convert ‘multiqc_data.json’ files, produced by the wonderful ‘MultiQC’ tool, into tidy data frames for downstream analysis in R.

Please visit the pkgdown website for a comprehensive tutorial and function documentation.

Installation

The latest stable version can be installed from CRAN:

install.packages("TidyMultiqc")

You can also install the development version of TidyMultiqc fromGitHub with:

install.packages("devtools")

devtools::install_github("multimeric/TidyMultiqc")

Example

TidyMultiqc::load_multiqc(multiqc_data_path) #> # A tibble: 6 × 165 #> metadata.sample_id general.total_reads general.mapped_reads general.percentag… #> #> 1 P4107_1003 868204107 847562410 97.6 #> 2 P4107_1004 1002828927 985115356 98.2 #> 3 P4107_1005 974955793 955921317 98.0 #> 4 P4107_1002 865975844 847067526 97.8 #> 5 P4107_1006 912383669 894970438 98.1 #> 6 P4107_1001 772071557 751147332 97.3 #> # … with 161 more variables: general.median_coverage , #> # general.median_insert_size , general.avg_gc , #> # general.1_x_pc , general.5_x_pc , general.10_x_pc , #> # general.30_x_pc , general.50_x_pc , general.genome , #> # general.number_of_variants_before_filter , #> # general.number_of_known_variants_brie_non_empty_id , #> # general.number_of_known_variants_brie_non_empty_id_percent , …