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.
The latest stable version can be installed from CRAN:
install.packages("TidyMultiqc")You can also install the development version of TidyMultiqc from GitHub with:
# install.packages("devtools")
devtools::install_github("multimeric/TidyMultiqc")
TidyMultiqc::load_multiqc(multiqc_data_path)
#> # A tibble: 6 × 165
#> metadata.sample_id general.total_reads general.mapped_reads general.percentag…
#> <chr> <dbl> <dbl> <dbl>
#> 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 <int>,
#> # general.median_insert_size <int>, general.avg_gc <dbl>,
#> # general.1_x_pc <dbl>, general.5_x_pc <dbl>, general.10_x_pc <dbl>,
#> # general.30_x_pc <dbl>, general.50_x_pc <dbl>, general.genome <chr>,
#> # general.number_of_variants_before_filter <dbl>,
#> # general.number_of_known_variants_brie_non_empty_id <dbl>,
#> # general.number_of_known_variants_brie_non_empty_id_percent <dbl>, …