From 9b3fa584be0e0cb7b0968d973007ab27afb19cea Mon Sep 17 00:00:00 2001
From: js2264 <jacquesserizay@gmail.com>
Date: Tue, 7 Nov 2023 18:35:41 +0100
Subject: [PATCH] fix: remove hicrep dependency

---
 .github/workflows/rworkflows.yml | 10 ------
 DESCRIPTION                      |  3 --
 inst/index.qmd                   |  1 +
 inst/pages/interoperability.qmd  | 60 ++------------------------------
 inst/pages/workflow-centros.qmd  |  1 -
 inst/pages/workflow-yeast.qmd    |  1 -
 6 files changed, 3 insertions(+), 73 deletions(-)

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`
+<!-- - `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)
 ```