In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

knitr::opts_chunk$set(echo = TRUE)

QC Summary {.tabset}

InsertSize

Short Fragments

cat("![](",'ShortFragmentFraction.png',")")

InsertSize Distribution

plots <- list.files(".","fragmentSize_.*png$")
   for(i in 1:length(plots)){
      filename <- plots[i]
      cat("![](",filename,")")
   }

chrM Content

plots2 <- list.files(".","ChrM.*png$")
   for(i in 1:length(plots2)){
      filename2 <- plots2[i]
      cat("![](",filename2,")")
    }

Enrichment around TSS

Mono-Nucleosomal

plots <- list.files(".","heatmap_TSS.*monoNucl.png$")
plots2 <- list.files(".","lineplot_TSS.*monoNucl.png$")
   for(i in 1:length(plots2)){
      filename <- plots2[i]
      cat("![](",filename,")")
   }

   for(i in 1:length(plots)){
      filename <- plots[i]
      cat("![](",filename,")")
   }

Sub-Nucleosomal

plots <- list.files(".","heatmap_TSS.*subNucl.png$")
plots2 <- list.files(".","lineplot_TSS.*subNucl.png$")
   for(i in 1:length(plots2)){
      filename <- plots2[i]
      cat("![](",filename,")")
   }

   for(i in 1:length(plots)){
      filename <- plots[i]
      cat("![](",filename,")")
   }

Multi-Nucleosomal

plots <- list.files(".","heatmap_TSS.*multiNucl.png$")
plots2 <- list.files(".","lineplot_TSS.*multiNucl.png$")
   for(i in 1:length(plots2)){
      filename <- plots2[i]
      cat("![](",filename,")")
   }

   for(i in 1:length(plots)){
      filename <- plots[i]
      cat("![](",filename,")")
   }

Per-Sample-Plots

plots <- list.files(".","lineplot_TSS.*bam.png$")
   for(i in 1:length(plots)){
      filename <- plots[i]
      cat("![](",filename,")")
   }

Enrichment around CTCF binding motifs

Mono-Nucleosomal

plots <- list.files(".","heatmap_CTCF.*monoNucl.png$")
plots2 <- list.files(".","lineplot_CTCF.*monoNucl.png$")
  for(i in 1:length(plots2)){
      filename <- plots2[i]
      cat("![](",filename,")")
   }

   for(i in 1:length(plots)){
      filename <- plots[i]
      cat("![](",filename,")")
   }

Sub-Nucleosomal

plots <- list.files(".","heatmap_CTCF.*subNucl.png$")
plots2 <- list.files(".","lineplot_CTCF.*subNucl.png$")
   for(i in 1:length(plots2)){
      filename <- plots2[i]
      cat("![](",filename,")")
   }

   for(i in 1:length(plots)){
      filename <- plots[i]
      cat("![](",filename,")")
   }

Multi-Nucleosomal

plots <- list.files(".","heatmap_CTCF.*multiNucl.png$")
plots2 <- list.files(".","lineplot_CTCF.*multiNucl.png$")
  for(i in 1:length(plots2)){
      filename <- plots2[i]
      cat("![](",filename,")")
   }

   for(i in 1:length(plots)){
      filename <- plots[i]
      cat("![](",filename,")")
   }

Per-Sample-Plots

plots <- list.files(".","lineplot_CTCF.*bam.png$")
   for(i in 1:length(plots)){
      filename <- plots[i]
      cat("![](",filename,")")
   }

SessionInfo

sessionInfo()

uzh/ezRun documentation built on May 4, 2024, 3:23 p.m.