From 917b96cef74ba74294e1eeaf9f20d5cec1dddb7c 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: Fri, 28 Oct 2022 07:02:35 +0200
Subject: [PATCH] gnu: Add r-debcam.

* gnu/packages/bioconductor.scm (r-debcam): New variable.
---
 gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b8535250f9..23d7d5b3bf 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -48,6 +48,7 @@ (define-module (gnu packages bioconductor)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages java)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages netpbm)
   #:use-module (gnu packages python)
@@ -3051,6 +3052,45 @@ (define-public r-dearseq
 set analyses, and can deal with repeated or longitudinal data.")
     (license license:gpl2)))
 
+(define-public r-debcam
+  (package
+    (name "r-debcam")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "debCAM" version))
+              (sha256
+               (base32
+                "1ynz57kkxl8nx80zhh1vhhydqb5n6r9d7p69f0k9nj8rp4hdgng7"))))
+    (properties `((upstream-name . "debCAM")))
+    (build-system r-build-system)
+    (inputs (list openjdk))
+    (propagated-inputs
+     (list r-apcluster
+           r-biobase
+           r-biocparallel
+           r-corpcor
+           r-dmwr2
+           r-geometry
+           r-nmf
+           r-nnls
+           r-pcapp
+           r-rjava
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/debCAM")
+    (synopsis "Deconvolution by convex analysis of mixtures")
+    (description
+     "This package is an R implementation for fully unsupervised deconvolution
+of complex tissues.  DebCAM provides basic functions to perform unsupervised
+deconvolution on mixture expression profiles by @acronym{CAM, Convex Analysis
+of Mixtures} and some auxiliary functions to help understand the
+subpopulation- specific results.  It also implements functions to perform
+supervised deconvolution based on prior knowledge of molecular markers, S
+matrix or A matrix.  Combining molecular markers from CAM and from prior
+knowledge can achieve semi-supervised deconvolution of mixtures.")
+    (license license:gpl2)))
+
 (define-public r-decipher
   (package
     (name "r-decipher")