diff --git a/OHCA.scss b/OHCA.scss index 1f4fa82..623b06f 100644 --- a/OHCA.scss +++ b/OHCA.scss @@ -77,7 +77,7 @@ h1, .h1, h2, .h2, h3, .h3, h4, .h4, h5, .h5 { /* Put a border around session info print ------------------------------------------------ */ #session-info code, p+ pre code { - border: 1px solid black + // border: 1px solid black } /* Code colors ------------------------------------------------------------------------- */ diff --git a/index.qmd b/index.qmd index 24ab15f..f0e171c 100644 --- a/index.qmd +++ b/index.qmd @@ -21,10 +21,6 @@ starts with key concepts important for the analysis of chromatin conformation ca presents `Bioconductor` tools that can be leveraged to process, analyze, explore and visualize Hi-C data. -::: {.callout-caution} -This project is currently under active development. Several sections of this book may not be accurate, as the packages introduced in this book are still maturing. -::: - ::: {.content-hidden when-format="pdf"} # Table of contents {-} diff --git a/topological-features.qmd b/topological-features.qmd index 1962721..678704d 100644 --- a/topological-features.qmd +++ b/topological-features.qmd @@ -5,11 +5,6 @@ bibliography: bibliography.bib # Finding topological features in Hi-C -::: {.callout-warning} -## Page under construction -A number of sections in this page still need to be completed. -::: - ```{r} #| echo: false #| results: "hide" @@ -108,6 +103,7 @@ file), the `export` function can be used: ```{r} library(GenomicRanges) +library(rtracklayer) coverage(metadata(microC_compts)$eigens, weight = 'eigen') |> export('microC_eigen.bw') topologicalFeatures(microC_compts, "compartments") |> export('microC_compartments.gff3') ``` @@ -155,8 +151,7 @@ pairwise eigenvector quantiles and plotted in a 2D heatmap. ```{r} library(BiocParallel) -bpparam <- SerialParam(progressbar = FALSE) -plotSaddle(microC_compts, nbins = 25, BPPARAM = bpparam) +plotSaddle(microC_compts, nbins = 25, BPPARAM = SerialParam(progressbar = FALSE)) ``` Here, the top-left small corner represents average O/E scores between strong B