From b0dd06bd0caea46a852248ab48ab2e6aaff57752 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?=
 <madalinionel.patrascu@mdc-berlin.de>
Date: Mon, 11 Apr 2022 16:03:35 +0200
Subject: [PATCH] gnu: Add r-xcir.

* gnu/packages/bioconductor.scm (r-xcir): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 39 ++++++++++++++++++++++++++++++++++-
 1 file changed, 38 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2fa64c4b0b..bec3496057 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7,7 +7,7 @@
 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
-;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
@@ -5191,6 +5191,43 @@ (define-public r-vsn
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
+;; There is no source tarball, so we fetch the code from the Bioconductor git
+;; repository.
+(define-public r-xcir
+  (let ((commit "3b59d456f2ad7f70285915b036b1dc4279687277")
+        (revision "1"))
+    (package
+      (name "r-xcir")
+      (version (git-version "1.8.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.bioconductor.org/packages/XCIR")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1xxw5ady5j2p7z7zjxgx7lhm85x7fxbljiv49lc2ghsvh9wm937p"))))
+      (properties `((upstream-name . "XCIR")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-biomart
+                               r-biostrings
+                               r-data-table
+                               r-ggplot2
+                               r-iranges
+                               r-readxl
+                               r-s4vectors
+                               r-seqminer
+                               r-variantannotation))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/SRenan/XCIR")
+      (synopsis "Analysis of X chromosome inactivation")
+      (description
+       "This package is an R package that offers models and tools for subject
+level analysis of @dfn{X chromosome inactivation} (XCI) and XCI-escape
+inference.")
+      (license license:gpl2))))
+
 (define-public r-xina
   (package
     (name "r-xina")