diff --git a/src/metrics/ks_statistic_gene_cell/config.vsh.yaml b/src/metrics/ks_statistic_gene_cell/config.vsh.yaml index 0770b0c3..3edf6105 100644 --- a/src/metrics/ks_statistic_gene_cell/config.vsh.yaml +++ b/src/metrics/ks_statistic_gene_cell/config.vsh.yaml @@ -1,12 +1,12 @@ __merge__: ../../api/comp_metric.yaml -name: ks_statistic +name: ks_statistic_gene_cell info: metrics: - name: ks_statistic_frac_zero_genes label: Fraction of zeros in genes - summary: Ks Statistic of the fraction of zeroes in the genes + summary: KS Statistic of the fraction of zeroes in the genes description: | The Kolmogorov-Smirnov statistic comparing the fraction of zeros in the genes of the real counts versus the fraction of zeros in the genes of @@ -19,7 +19,7 @@ info: maximize: false - name: ks_statistic_frac_zero_cells label: Fraction of zeros in cells - summary: Ks Statistic of the fraction of zeroes in the cells + summary: KS Statistic of the fraction of zeroes in the cells description: | The Kolmogorov-Smirnov statistic comparing the fraction of zeros in the cells of the real counts versus the fraction of zeros in the cells of @@ -39,11 +39,16 @@ engines: - type: docker image: ghcr.io/openproblems-bio/base_images/r:1.1.0 setup: - - type: r - cran: ks + - type: apt + packages: + - git + - r-bioc-edger + - r-cran-ks + - r-cran-resample + - r-cran-reshape2 runners: - type: executable - type: nextflow directives: - label: [midtime,midmem,midcpu] + label: [midtime, midmem, midcpu] diff --git a/src/metrics/ks_statistic_gene_cell/script.R b/src/metrics/ks_statistic_gene_cell/script.R index b7ee3ade..503d0f47 100644 --- a/src/metrics/ks_statistic_gene_cell/script.R +++ b/src/metrics/ks_statistic_gene_cell/script.R @@ -1,4 +1,8 @@ requireNamespace("anndata", quietly = TRUE) +requireNamespace("edgeR", quietly = TRUE) +requireNamespace("ks", quietly = TRUE) +requireNamespace("resample", quietly = TRUE) +requireNamespace("reshape2", quietly = TRUE) ## VIASH START par <- list(