diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index 0df685c..7f2fd36 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -25,16 +25,6 @@ jobs: r: auto cont: ghcr.io/bioconductor/bioconductor:devel rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release - # - os: macOS-latest - # bioc: release - # r: auto - # cont: ~ - # rspm: ~ - # - os: windows-latest - # bioc: release - # r: auto - # cont: ~ - # rspm: ~ steps: - uses: neurogenomics/rworkflows@master with: diff --git a/DESCRIPTION b/DESCRIPTION index fd959e5..1bb5a5e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -27,7 +27,6 @@ Imports: WGCNA, diffHic, strawr, - hicrep, multiHiCcompare, TopDom, GOTHiC, @@ -41,8 +40,6 @@ Imports: quarto, sessioninfo Suggests: -Remotes: - github::TaoYang-dev/hicrep biocViews: HiC, DNA3DStructure diff --git a/inst/index.qmd b/inst/index.qmd index 59e7d2b..01de44d 100644 --- a/inst/index.qmd +++ b/inst/index.qmd @@ -182,6 +182,7 @@ aforementioned packages pre-installed, and initiate an interactive R session. The OHCA book has been rendered in R thanks to a number of packages, including but not only: +- **`BiocBook`** - `devtools` - `quarto` - `rebook` diff --git a/inst/pages/interoperability.qmd b/inst/pages/interoperability.qmd index 66b9c81..161b2a5 100644 --- a/inst/pages/interoperability.qmd +++ b/inst/pages/interoperability.qmd @@ -9,7 +9,7 @@ This notebook illustrates how to use a range of popular Hi-C—related `R` packa following packages is illustrated here: - `diffHic` -- `hicrep` + - `multiHiCcompare` - `TopDom` - `GOTHiC` @@ -29,7 +29,7 @@ library(InteractionSet) library(HiCExperiment) library(HiContactsData) library(plyinteractions) -library(hicrep) +# library(hicrep) library(multiHiCcompare) library(dplyr) library(tidyr) @@ -128,62 +128,6 @@ p + geom_rect( ) ``` -## HiCrep - -`hicrep` is a popular package to compute **stratum-adjusted correlations** between Hi-C datasets (@Yang_2017). -"Stratum" refers to the distance from the main diagonal: with increase distance from the main diagonal, -interactions of the DNA polymer are bound to decrease. `hicrep` computes a "per-stratum" correlation score and -computes a weighted average correlation for entire chromosomes. - -::: {.callout-tip} - -### Installing `hicrep` - -`hicrep` package has been available from Bioconductor for many years but has -been withdrawn from their repositories at some point. You can always install -`hicrep` directly from its GitHub repository as follows: - -```{r} -#| eval: false -remotes::install_github('TaoYang-dev/hicrep') -``` - -::: - -In order to use `hicrep`, we first need to create two `HiCExperiment` objects. - -```{r eval = FALSE} -# ---- This downloads example `.mcool` files and caches them locally -coolf_eco1 <- HiContactsData('yeast_eco1', 'mcool') -``` - -```{r} -hic_wt <- import(coolf_wt, format = 'cool') -hic_eco1 <- import(coolf_eco1, format = 'cool') -``` - -We can now run the main `get.scc` function from `hicrep`. The documentation -for this function is available from the console by typing `?hicrep::get.scc`. -More information is also available from the [GitHub page](https://github.com/TaoYang-dev/hicrep#compute-reproducibility-score-using-hicrep). It informs the end user that -the input for this function should be two intra-chromosomal Hi-C **raw count** matrices -in square (optionally sparse) format. - -```{r} -hic_wt - -as.matrix(hic_wt["IV"], use.scores = 'count')[1:10, 1:10] - -library(hicrep) -scc <- get.scc( - as.matrix(hic_wt["IV"], use.scores = 'count'), - as.matrix(hic_eco1["IV"], use.scores = 'count'), - resol = 1000, h = 25, lbr = 5000, ubr = 50000 -) -scc - -scc$scc -``` - ## multiHiCcompare The `multiHiCcompare` package provides functions for joint diff --git a/inst/pages/workflow-centros.qmd b/inst/pages/workflow-centros.qmd index 829ecf8..c7094ad 100644 --- a/inst/pages/workflow-centros.qmd +++ b/inst/pages/workflow-centros.qmd @@ -11,7 +11,6 @@ library(GenomicRanges) library(InteractionSet) library(HiCExperiment) library(HiContactsData) -library(hicrep) library(multiHiCcompare) ``` diff --git a/inst/pages/workflow-yeast.qmd b/inst/pages/workflow-yeast.qmd index ee9c515..738204b 100644 --- a/inst/pages/workflow-yeast.qmd +++ b/inst/pages/workflow-yeast.qmd @@ -11,7 +11,6 @@ library(GenomicRanges) library(InteractionSet) library(HiCExperiment) library(HiContactsData) -library(hicrep) library(multiHiCcompare) ```