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Subject: [bug#47223] [PATCH] r-signac and r-chromstardata
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--0000000000001de91c05bdc47c1d
Content-Type: text/plain; charset="UTF-8"

Dear Guixer,

Can you please add these two r packages in guix? Thanks in advance.
I am not sure how to create this patch, and this is what I did:

guix import cran -a git -r 'https://github.com/timoast/signac/'

(define-public r-signac
  (let ((commit
          "e0512d348adeda4a3f23a2e8f56d1fe09840e03c")
        (revision "1"))
    (package
      (name "r-signac")
      (version (git-version "1.1.1" revision commit))
      (source
        (origin
          (method git-fetch)
          (uri (git-reference
                 (url "https://github.com/timoast/signac/")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
            (base32
              "1yihhrv7zs87ax61la1nb4y12lg3knraw4b20k5digbcwm8488lb"))))
      (properties `((upstream-name . "Signac")))
      (build-system r-build-system)
      (inputs `(("zlib" ,zlib)))
      (propagated-inputs
        `(("r-annotationfilter" ,r-annotationfilter)
          ("r-biocgenerics" ,r-biocgenerics)
          ("r-biostrings" ,r-biostrings)
          ("r-biovizbase" ,r-biovizbase)
          ("r-data-table" ,r-data-table)
          ("r-dplyr" ,r-dplyr)
          ("r-fastmatch" ,r-fastmatch)
          ("r-future" ,r-future)
          ("r-future-apply" ,r-future-apply)
          ("r-genomeinfodb" ,r-genomeinfodb)
          ("r-genomicranges" ,r-genomicranges)
          ("r-ggbio" ,r-ggbio)
          ("r-ggforce" ,r-ggforce)
          ("r-ggplot2" ,r-ggplot2)
          ("r-ggrepel" ,r-ggrepel)
          ("r-ggseqlogo" ,r-ggseqlogo)
          ("r-iranges" ,r-iranges)
          ("r-irlba" ,r-irlba)
          ("r-lsa" ,r-lsa)
          ("r-matrix" ,r-matrix)
          ("r-patchwork" ,r-patchwork)
          ("r-pbapply" ,r-pbapply)
          ("r-rcpp" ,r-rcpp)
          ("r-rcpproll" ,r-rcpproll)
          ("r-rsamtools" ,r-rsamtools)
          ("r-s4vectors" ,r-s4vectors)
          ("r-scales" ,r-scales)
          ("r-seurat" ,r-seurat)
          ("r-seuratobject" ,r-seuratobject)
          ("r-stringi" ,r-stringi)
          ("r-tidyr" ,r-tidyr)))
      (home-page "https://github.com/timoast/signac/")
      (synopsis
        "Analysis of Single-Cell Chromatin Data")
      (description
        "This package provides a framework for the analysis and exploration
of single-cell chromatin data.  The 'Signac' package contains functions for
quantifying single-cell chromatin data, computing per-cell quality control
metrics, dimension reduction and normalization, visualization, and DNA
sequence motif analysis.  Reference: Stuart et al. (2020)
<doi:10.1101/2020.11.09.373613>.")
      (license expat))))

guix import cran -a git -r 'https://git.bioconductor.org/packages/chromstaR'

(define-public r-chromstardata
  (package
    (name "r-chromstardata")
    (version "1.16.0")
    (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri
               "chromstaRData"
               version
               'experiment))
        (sha256
          (base32
            "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab"))))
    (properties `((upstream-name . "chromstaRData")))
    (build-system r-build-system)
    (home-page
      "https://bioconductor.org/packages/chromstaRData")
    (synopsis
      "ChIP-seq data for Demonstration Purposes")
    (description
      "ChIP-seq data for demonstration purposes in the chromstaR package.")
    (license gpl3)))

(define-public r-chromstar
  (let ((commit
          "16c0394a3a0857a050237d2b8b33cd02d92d6239")
        (revision "1"))
    (package
      (name "r-chromstar")
      (version (git-version "1.17.0" revision commit))
      (source
        (origin
          (method git-fetch)
          (uri (git-reference
                 (url "https://git.bioconductor.org/packages/chromstaR")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
            (base32
              "0wr6wlz3z3x21c25hgczalswicrqfhw00wmsa9jjd42w4hj5lkh9"))))
      (properties `((upstream-name . "chromstaR")))
      (build-system r-build-system)
      (propagated-inputs
        `(("r-bamsignals" ,r-bamsignals)
          ("r-biocgenerics" ,r-biocgenerics)
          ("r-chromstardata" ,r-chromstardata)
          ("r-doparallel" ,r-doparallel)
          ("r-foreach" ,r-foreach)
          ("r-genomeinfodb" ,r-genomeinfodb)
          ("r-genomicalignments" ,r-genomicalignments)
          ("r-genomicranges" ,r-genomicranges)
          ("r-ggplot2" ,r-ggplot2)
          ("r-iranges" ,r-iranges)
          ("r-mvtnorm" ,r-mvtnorm)
          ("r-reshape2" ,r-reshape2)
          ("r-rsamtools" ,r-rsamtools)
          ("r-s4vectors" ,r-s4vectors)))
      (native-inputs `(("r-knitr" ,r-knitr)))
      (home-page
        "https://git.bioconductor.org/packages/chromstaR")
      (synopsis
        "Combinatorial and Differential Chromatin State Analysis for
ChIP-Seq Data")
      (description
        "This package implements functions for combinatorial and
differential analysis of ChIP-seq data.  It includes uni- and multivariate
peak-calling, export to genome browser viewable files, and functi
ons for enrichment analyses.")
      (license artistic2.0))))

with best regards,
Hong Li

--0000000000001de91c05bdc47c1d
Content-Type: text/html; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr">Dear Guixer,<br><br><div>Can you please add these two r pa=
ckages in guix? Thanks in advance.</div><div>I am not sure how to create th=
is patch, and this is what I did:</div><br><span style=3D"color:rgb(0,0,255=
)">guix import cran -a git -r &#39;<a href=3D"https://github.com/timoast/si=
gnac/">https://github.com/timoast/signac/</a>&#39;</span><br><br>(define-pu=
blic r-signac<br>=C2=A0 (let ((commit<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=
 &quot;e0512d348adeda4a3f23a2e8f56d1fe09840e03c&quot;)<br>=C2=A0 =C2=A0 =C2=
=A0 =C2=A0 (revision &quot;1&quot;))<br>=C2=A0 =C2=A0 (package<br>=C2=A0 =
=C2=A0 =C2=A0 (name &quot;r-signac&quot;)<br>=C2=A0 =C2=A0 =C2=A0 (version =
(git-version &quot;1.1.1&quot; revision commit))<br>=C2=A0 =C2=A0 =C2=A0 (s=
ource<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 (origin<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0=
 =C2=A0 (method git-fetch)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (uri (git-=
reference<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=
(url &quot;<a href=3D"https://github.com/timoast/signac/">https://github.co=
m/timoast/signac/</a>&quot;)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0(commit commit)))<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=
 (file-name (git-file-name name version))<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =
=C2=A0 (sha256<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (base32<br>=C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 &quot;1yihhrv7zs87ax61la1nb4y=
12lg3knraw4b20k5digbcwm8488lb&quot;))))<br>=C2=A0 =C2=A0 =C2=A0 (properties=
 `((upstream-name . &quot;Signac&quot;)))<br>=C2=A0 =C2=A0 =C2=A0 (build-sy=
stem r-build-system)<br>=C2=A0 =C2=A0 =C2=A0 (inputs `((&quot;zlib&quot; ,z=
lib)))<br>=C2=A0 =C2=A0 =C2=A0 (propagated-inputs<br>=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 `((&quot;r-annotationfilter&quot; ,r-annotationfilter)<br>=C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-biocgenerics&quot; ,r-biocgenerics)<br>=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-biostrings&quot; ,r-biostrings)=
<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-biovizbase&quot; ,r-biovizb=
ase)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-data-table&quot; ,r-dat=
a-table)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-dplyr&quot; ,r-dply=
r)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-fastmatch&quot; ,r-fastma=
tch)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-future&quot; ,r-future)=
<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-future-apply&quot; ,r-futur=
e-apply)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-genomeinfodb&quot; =
,r-genomeinfodb)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-genomicrang=
es&quot; ,r-genomicranges)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-g=
gbio&quot; ,r-ggbio)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-ggforce=
&quot; ,r-ggforce)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-ggplot2&q=
uot; ,r-ggplot2)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-ggrepel&quo=
t; ,r-ggrepel)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-ggseqlogo&quo=
t; ,r-ggseqlogo)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-iranges&quo=
t; ,r-iranges)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-irlba&quot; ,=
r-irlba)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-lsa&quot; ,r-lsa)<b=
r>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-matrix&quot; ,r-matrix)<br>=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-patchwork&quot; ,r-patchwork)<b=
r>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-pbapply&quot; ,r-pbapply)<br>=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-rcpp&quot; ,r-rcpp)<br>=C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-rcpproll&quot; ,r-rcpproll)<br>=C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-rsamtools&quot; ,r-rsamtools)<br>=C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-s4vectors&quot; ,r-s4vectors)<br>=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-scales&quot; ,r-scales)<br>=C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-seurat&quot; ,r-seurat)<br>=C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-seuratobject&quot; ,r-seuratobject)<br=
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-stringi&quot; ,r-stringi)<br>=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-tidyr&quot; ,r-tidyr)))<br>=C2=
=A0 =C2=A0 =C2=A0 (home-page &quot;<a href=3D"https://github.com/timoast/si=
gnac/">https://github.com/timoast/signac/</a>&quot;)<br>=C2=A0 =C2=A0 =C2=
=A0 (synopsis<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 &quot;Analysis of Single-Cell =
Chromatin Data&quot;)<br>=C2=A0 =C2=A0 =C2=A0 (description<br>=C2=A0 =C2=A0=
 =C2=A0 =C2=A0 &quot;This package provides a framework for the analysis and=
 exploration of single-cell chromatin data.=C2=A0 The &#39;Signac&#39; pack=
age contains functions for quantifying single-cell chromatin data, computin=
g per-cell quality control metrics, dimension reduction and normalization, =
visualization, and DNA sequence motif analysis.=C2=A0 Reference: Stuart et =
al. (2020) &lt;doi:10.1101/2020.11.09.373613&gt;.&quot;)<br>=C2=A0 =C2=A0 =
=C2=A0 (license expat))))<br><br><span style=3D"color:rgb(0,0,255)">guix im=
port cran -a git -r &#39;<a href=3D"https://git.bioconductor.org/packages/c=
hromstaR">https://git.bioconductor.org/packages/chromstaR</a>&#39;</span><b=
r><br>(define-public r-chromstardata<br>=C2=A0 (package<br>=C2=A0 =C2=A0 (n=
ame &quot;r-chromstardata&quot;)<br>=C2=A0 =C2=A0 (version &quot;1.16.0&quo=
t;)<br>=C2=A0 =C2=A0 (source<br>=C2=A0 =C2=A0 =C2=A0 (origin<br>=C2=A0 =C2=
=A0 =C2=A0 =C2=A0 (method url-fetch)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 (uri (b=
ioconductor-uri<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0&=
quot;chromstaRData&quot;<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0version<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0&#39;experiment))<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 (sha256<br>=C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 (base32<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 &quot;0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab&quot;))))<br=
>=C2=A0 =C2=A0 (properties `((upstream-name . &quot;chromstaRData&quot;)))<=
br>=C2=A0 =C2=A0 (build-system r-build-system)<br>=C2=A0 =C2=A0 (home-page<=
br>=C2=A0 =C2=A0 =C2=A0 &quot;<a href=3D"https://bioconductor.org/packages/=
chromstaRData">https://bioconductor.org/packages/chromstaRData</a>&quot;)<b=
r>=C2=A0 =C2=A0 (synopsis<br>=C2=A0 =C2=A0 =C2=A0 &quot;ChIP-seq data for D=
emonstration Purposes&quot;)<br>=C2=A0 =C2=A0 (description<br>=C2=A0 =C2=A0=
 =C2=A0 &quot;ChIP-seq data for demonstration purposes in the chromstaR pac=
kage.&quot;)<br>=C2=A0 =C2=A0 (license gpl3)))<br><br>(define-public r-chro=
mstar<br>=C2=A0 (let ((commit<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 &quot;1=
6c0394a3a0857a050237d2b8b33cd02d92d6239&quot;)<br>=C2=A0 =C2=A0 =C2=A0 =C2=
=A0 (revision &quot;1&quot;))<br>=C2=A0 =C2=A0 (package<br>=C2=A0 =C2=A0 =
=C2=A0 (name &quot;r-chromstar&quot;)<br>=C2=A0 =C2=A0 =C2=A0 (version (git=
-version &quot;1.17.0&quot; revision commit))<br>=C2=A0 =C2=A0 =C2=A0 (sour=
ce<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 (origin<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =
=C2=A0 (method git-fetch)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (uri (git-r=
eference<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(=
url &quot;<a href=3D"https://git.bioconductor.org/packages/chromstaR">https=
://git.bioconductor.org/packages/chromstaR</a>&quot;)<br>=C2=A0 =C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(commit commit)))<br>=C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 (file-name (git-file-name name version))<br>=C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (sha256<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 (base32<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 &quo=
t;0wr6wlz3z3x21c25hgczalswicrqfhw00wmsa9jjd42w4hj5lkh9&quot;))))<br>=C2=A0 =
=C2=A0 =C2=A0 (properties `((upstream-name . &quot;chromstaR&quot;)))<br>=
=C2=A0 =C2=A0 =C2=A0 (build-system r-build-system)<br>=C2=A0 =C2=A0 =C2=A0 =
(propagated-inputs<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 `((&quot;r-bamsignals&quo=
t; ,r-bamsignals)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-biocgeneri=
cs&quot; ,r-biocgenerics)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-ch=
romstardata&quot; ,r-chromstardata)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (=
&quot;r-doparallel&quot; ,r-doparallel)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 (&quot;r-foreach&quot; ,r-foreach)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 (&quot;r-genomeinfodb&quot; ,r-genomeinfodb)<br>=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 (&quot;r-genomicalignments&quot; ,r-genomicalignments)<br>=C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-genomicranges&quot; ,r-genomicrang=
es)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-ggplot2&quot; ,r-ggplot2=
)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-iranges&quot; ,r-iranges)<=
br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-mvtnorm&quot; ,r-mvtnorm)<br=
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-reshape2&quot; ,r-reshape2)<br=
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-rsamtools&quot; ,r-rsamtools)<=
br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-s4vectors&quot; ,r-s4vectors=
)))<br>=C2=A0 =C2=A0 =C2=A0 (native-inputs `((&quot;r-knitr&quot; ,r-knitr)=
))<br>=C2=A0 =C2=A0 =C2=A0 (home-page<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 &quot;=
<a href=3D"https://git.bioconductor.org/packages/chromstaR">https://git.bio=
conductor.org/packages/chromstaR</a>&quot;)<br>=C2=A0 =C2=A0 =C2=A0 (synops=
is<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 &quot;Combinatorial and Differential Chro=
matin State Analysis for ChIP-Seq Data&quot;)<br>=C2=A0 =C2=A0 =C2=A0 (desc=
ription<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 &quot;This package implements functi=
ons for combinatorial and differential analysis of ChIP-seq data.=C2=A0 It =
includes uni- and multivariate peak-calling, export to genome browser viewa=
ble files, and functi<br>ons for enrichment analyses.&quot;)<br><div>=C2=A0=
 =C2=A0 =C2=A0 (license artistic2.0))))</div><div><br></div><div>with best =
regards,</div><div>Hong Li<br></div></div>

--0000000000001de91c05bdc47c1d--




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To: hong li <hongli520@gmail.com>
Subject: bug#47223: closed ([PATCH] r-signac and r-chromstardata)
Message-ID: <handler.47223.D47223.161641629218181.notifdone@debbugs.gnu.org>
References: <87czvrwesp.fsf@elephly.net>
 <CACnRHTgtbwrTq939iTxTkqeppBe6A+sJzxa1FsOkdocQu547zA@mail.gmail.com>
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Your bug report

#47223: [PATCH] r-signac and r-chromstardata

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 47223@debbugs.gnu.org.

--=20
47223: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D47223
GNU Bug Tracking System
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From: Ricardo Wurmus <rekado@elephly.net>
To: 47223-done@debbugs.gnu.org
Subject: [PATCH] r-signac and r-chromstardata
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Closing in favor of 47314.

-- 
Ricardo


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Subject: [PATCH] r-signac and r-chromstardata
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--0000000000001de91c05bdc47c1d
Content-Type: text/plain; charset="UTF-8"

Dear Guixer,

Can you please add these two r packages in guix? Thanks in advance.
I am not sure how to create this patch, and this is what I did:

guix import cran -a git -r 'https://github.com/timoast/signac/'

(define-public r-signac
  (let ((commit
          "e0512d348adeda4a3f23a2e8f56d1fe09840e03c")
        (revision "1"))
    (package
      (name "r-signac")
      (version (git-version "1.1.1" revision commit))
      (source
        (origin
          (method git-fetch)
          (uri (git-reference
                 (url "https://github.com/timoast/signac/")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
            (base32
              "1yihhrv7zs87ax61la1nb4y12lg3knraw4b20k5digbcwm8488lb"))))
      (properties `((upstream-name . "Signac")))
      (build-system r-build-system)
      (inputs `(("zlib" ,zlib)))
      (propagated-inputs
        `(("r-annotationfilter" ,r-annotationfilter)
          ("r-biocgenerics" ,r-biocgenerics)
          ("r-biostrings" ,r-biostrings)
          ("r-biovizbase" ,r-biovizbase)
          ("r-data-table" ,r-data-table)
          ("r-dplyr" ,r-dplyr)
          ("r-fastmatch" ,r-fastmatch)
          ("r-future" ,r-future)
          ("r-future-apply" ,r-future-apply)
          ("r-genomeinfodb" ,r-genomeinfodb)
          ("r-genomicranges" ,r-genomicranges)
          ("r-ggbio" ,r-ggbio)
          ("r-ggforce" ,r-ggforce)
          ("r-ggplot2" ,r-ggplot2)
          ("r-ggrepel" ,r-ggrepel)
          ("r-ggseqlogo" ,r-ggseqlogo)
          ("r-iranges" ,r-iranges)
          ("r-irlba" ,r-irlba)
          ("r-lsa" ,r-lsa)
          ("r-matrix" ,r-matrix)
          ("r-patchwork" ,r-patchwork)
          ("r-pbapply" ,r-pbapply)
          ("r-rcpp" ,r-rcpp)
          ("r-rcpproll" ,r-rcpproll)
          ("r-rsamtools" ,r-rsamtools)
          ("r-s4vectors" ,r-s4vectors)
          ("r-scales" ,r-scales)
          ("r-seurat" ,r-seurat)
          ("r-seuratobject" ,r-seuratobject)
          ("r-stringi" ,r-stringi)
          ("r-tidyr" ,r-tidyr)))
      (home-page "https://github.com/timoast/signac/")
      (synopsis
        "Analysis of Single-Cell Chromatin Data")
      (description
        "This package provides a framework for the analysis and exploration
of single-cell chromatin data.  The 'Signac' package contains functions for
quantifying single-cell chromatin data, computing per-cell quality control
metrics, dimension reduction and normalization, visualization, and DNA
sequence motif analysis.  Reference: Stuart et al. (2020)
<doi:10.1101/2020.11.09.373613>.")
      (license expat))))

guix import cran -a git -r 'https://git.bioconductor.org/packages/chromstaR'

(define-public r-chromstardata
  (package
    (name "r-chromstardata")
    (version "1.16.0")
    (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri
               "chromstaRData"
               version
               'experiment))
        (sha256
          (base32
            "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab"))))
    (properties `((upstream-name . "chromstaRData")))
    (build-system r-build-system)
    (home-page
      "https://bioconductor.org/packages/chromstaRData")
    (synopsis
      "ChIP-seq data for Demonstration Purposes")
    (description
      "ChIP-seq data for demonstration purposes in the chromstaR package.")
    (license gpl3)))

(define-public r-chromstar
  (let ((commit
          "16c0394a3a0857a050237d2b8b33cd02d92d6239")
        (revision "1"))
    (package
      (name "r-chromstar")
      (version (git-version "1.17.0" revision commit))
      (source
        (origin
          (method git-fetch)
          (uri (git-reference
                 (url "https://git.bioconductor.org/packages/chromstaR")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
            (base32
              "0wr6wlz3z3x21c25hgczalswicrqfhw00wmsa9jjd42w4hj5lkh9"))))
      (properties `((upstream-name . "chromstaR")))
      (build-system r-build-system)
      (propagated-inputs
        `(("r-bamsignals" ,r-bamsignals)
          ("r-biocgenerics" ,r-biocgenerics)
          ("r-chromstardata" ,r-chromstardata)
          ("r-doparallel" ,r-doparallel)
          ("r-foreach" ,r-foreach)
          ("r-genomeinfodb" ,r-genomeinfodb)
          ("r-genomicalignments" ,r-genomicalignments)
          ("r-genomicranges" ,r-genomicranges)
          ("r-ggplot2" ,r-ggplot2)
          ("r-iranges" ,r-iranges)
          ("r-mvtnorm" ,r-mvtnorm)
          ("r-reshape2" ,r-reshape2)
          ("r-rsamtools" ,r-rsamtools)
          ("r-s4vectors" ,r-s4vectors)))
      (native-inputs `(("r-knitr" ,r-knitr)))
      (home-page
        "https://git.bioconductor.org/packages/chromstaR")
      (synopsis
        "Combinatorial and Differential Chromatin State Analysis for
ChIP-Seq Data")
      (description
        "This package implements functions for combinatorial and
differential analysis of ChIP-seq data.  It includes uni- and multivariate
peak-calling, export to genome browser viewable files, and functi
ons for enrichment analyses.")
      (license artistic2.0))))

with best regards,
Hong Li

--0000000000001de91c05bdc47c1d
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Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr">Dear Guixer,<br><br><div>Can you please add these two r pa=
ckages in guix? Thanks in advance.</div><div>I am not sure how to create th=
is patch, and this is what I did:</div><br><span style=3D"color:rgb(0,0,255=
)">guix import cran -a git -r &#39;<a href=3D"https://github.com/timoast/si=
gnac/">https://github.com/timoast/signac/</a>&#39;</span><br><br>(define-pu=
blic r-signac<br>=C2=A0 (let ((commit<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=
 &quot;e0512d348adeda4a3f23a2e8f56d1fe09840e03c&quot;)<br>=C2=A0 =C2=A0 =C2=
=A0 =C2=A0 (revision &quot;1&quot;))<br>=C2=A0 =C2=A0 (package<br>=C2=A0 =
=C2=A0 =C2=A0 (name &quot;r-signac&quot;)<br>=C2=A0 =C2=A0 =C2=A0 (version =
(git-version &quot;1.1.1&quot; revision commit))<br>=C2=A0 =C2=A0 =C2=A0 (s=
ource<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 (origin<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0=
 =C2=A0 (method git-fetch)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (uri (git-=
reference<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=
(url &quot;<a href=3D"https://github.com/timoast/signac/">https://github.co=
m/timoast/signac/</a>&quot;)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0(commit commit)))<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=
 (file-name (git-file-name name version))<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =
=C2=A0 (sha256<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (base32<br>=C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 &quot;1yihhrv7zs87ax61la1nb4y=
12lg3knraw4b20k5digbcwm8488lb&quot;))))<br>=C2=A0 =C2=A0 =C2=A0 (properties=
 `((upstream-name . &quot;Signac&quot;)))<br>=C2=A0 =C2=A0 =C2=A0 (build-sy=
stem r-build-system)<br>=C2=A0 =C2=A0 =C2=A0 (inputs `((&quot;zlib&quot; ,z=
lib)))<br>=C2=A0 =C2=A0 =C2=A0 (propagated-inputs<br>=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 `((&quot;r-annotationfilter&quot; ,r-annotationfilter)<br>=C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-biocgenerics&quot; ,r-biocgenerics)<br>=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-biostrings&quot; ,r-biostrings)=
<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-biovizbase&quot; ,r-biovizb=
ase)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-data-table&quot; ,r-dat=
a-table)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-dplyr&quot; ,r-dply=
r)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-fastmatch&quot; ,r-fastma=
tch)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-future&quot; ,r-future)=
<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-future-apply&quot; ,r-futur=
e-apply)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-genomeinfodb&quot; =
,r-genomeinfodb)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-genomicrang=
es&quot; ,r-genomicranges)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-g=
gbio&quot; ,r-ggbio)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-ggforce=
&quot; ,r-ggforce)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-ggplot2&q=
uot; ,r-ggplot2)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-ggrepel&quo=
t; ,r-ggrepel)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-ggseqlogo&quo=
t; ,r-ggseqlogo)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-iranges&quo=
t; ,r-iranges)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-irlba&quot; ,=
r-irlba)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-lsa&quot; ,r-lsa)<b=
r>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-matrix&quot; ,r-matrix)<br>=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-patchwork&quot; ,r-patchwork)<b=
r>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-pbapply&quot; ,r-pbapply)<br>=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-rcpp&quot; ,r-rcpp)<br>=C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-rcpproll&quot; ,r-rcpproll)<br>=C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-rsamtools&quot; ,r-rsamtools)<br>=C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-s4vectors&quot; ,r-s4vectors)<br>=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-scales&quot; ,r-scales)<br>=C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-seurat&quot; ,r-seurat)<br>=C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-seuratobject&quot; ,r-seuratobject)<br=
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-stringi&quot; ,r-stringi)<br>=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-tidyr&quot; ,r-tidyr)))<br>=C2=
=A0 =C2=A0 =C2=A0 (home-page &quot;<a href=3D"https://github.com/timoast/si=
gnac/">https://github.com/timoast/signac/</a>&quot;)<br>=C2=A0 =C2=A0 =C2=
=A0 (synopsis<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 &quot;Analysis of Single-Cell =
Chromatin Data&quot;)<br>=C2=A0 =C2=A0 =C2=A0 (description<br>=C2=A0 =C2=A0=
 =C2=A0 =C2=A0 &quot;This package provides a framework for the analysis and=
 exploration of single-cell chromatin data.=C2=A0 The &#39;Signac&#39; pack=
age contains functions for quantifying single-cell chromatin data, computin=
g per-cell quality control metrics, dimension reduction and normalization, =
visualization, and DNA sequence motif analysis.=C2=A0 Reference: Stuart et =
al. (2020) &lt;doi:10.1101/2020.11.09.373613&gt;.&quot;)<br>=C2=A0 =C2=A0 =
=C2=A0 (license expat))))<br><br><span style=3D"color:rgb(0,0,255)">guix im=
port cran -a git -r &#39;<a href=3D"https://git.bioconductor.org/packages/c=
hromstaR">https://git.bioconductor.org/packages/chromstaR</a>&#39;</span><b=
r><br>(define-public r-chromstardata<br>=C2=A0 (package<br>=C2=A0 =C2=A0 (n=
ame &quot;r-chromstardata&quot;)<br>=C2=A0 =C2=A0 (version &quot;1.16.0&quo=
t;)<br>=C2=A0 =C2=A0 (source<br>=C2=A0 =C2=A0 =C2=A0 (origin<br>=C2=A0 =C2=
=A0 =C2=A0 =C2=A0 (method url-fetch)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 (uri (b=
ioconductor-uri<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0&=
quot;chromstaRData&quot;<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0version<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0&#39;experiment))<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 (sha256<br>=C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 (base32<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 &quot;0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab&quot;))))<br=
>=C2=A0 =C2=A0 (properties `((upstream-name . &quot;chromstaRData&quot;)))<=
br>=C2=A0 =C2=A0 (build-system r-build-system)<br>=C2=A0 =C2=A0 (home-page<=
br>=C2=A0 =C2=A0 =C2=A0 &quot;<a href=3D"https://bioconductor.org/packages/=
chromstaRData">https://bioconductor.org/packages/chromstaRData</a>&quot;)<b=
r>=C2=A0 =C2=A0 (synopsis<br>=C2=A0 =C2=A0 =C2=A0 &quot;ChIP-seq data for D=
emonstration Purposes&quot;)<br>=C2=A0 =C2=A0 (description<br>=C2=A0 =C2=A0=
 =C2=A0 &quot;ChIP-seq data for demonstration purposes in the chromstaR pac=
kage.&quot;)<br>=C2=A0 =C2=A0 (license gpl3)))<br><br>(define-public r-chro=
mstar<br>=C2=A0 (let ((commit<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 &quot;1=
6c0394a3a0857a050237d2b8b33cd02d92d6239&quot;)<br>=C2=A0 =C2=A0 =C2=A0 =C2=
=A0 (revision &quot;1&quot;))<br>=C2=A0 =C2=A0 (package<br>=C2=A0 =C2=A0 =
=C2=A0 (name &quot;r-chromstar&quot;)<br>=C2=A0 =C2=A0 =C2=A0 (version (git=
-version &quot;1.17.0&quot; revision commit))<br>=C2=A0 =C2=A0 =C2=A0 (sour=
ce<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 (origin<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =
=C2=A0 (method git-fetch)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (uri (git-r=
eference<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(=
url &quot;<a href=3D"https://git.bioconductor.org/packages/chromstaR">https=
://git.bioconductor.org/packages/chromstaR</a>&quot;)<br>=C2=A0 =C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(commit commit)))<br>=C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 (file-name (git-file-name name version))<br>=C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (sha256<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 (base32<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 &quo=
t;0wr6wlz3z3x21c25hgczalswicrqfhw00wmsa9jjd42w4hj5lkh9&quot;))))<br>=C2=A0 =
=C2=A0 =C2=A0 (properties `((upstream-name . &quot;chromstaR&quot;)))<br>=
=C2=A0 =C2=A0 =C2=A0 (build-system r-build-system)<br>=C2=A0 =C2=A0 =C2=A0 =
(propagated-inputs<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 `((&quot;r-bamsignals&quo=
t; ,r-bamsignals)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-biocgeneri=
cs&quot; ,r-biocgenerics)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-ch=
romstardata&quot; ,r-chromstardata)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (=
&quot;r-doparallel&quot; ,r-doparallel)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 (&quot;r-foreach&quot; ,r-foreach)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 (&quot;r-genomeinfodb&quot; ,r-genomeinfodb)<br>=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 (&quot;r-genomicalignments&quot; ,r-genomicalignments)<br>=C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-genomicranges&quot; ,r-genomicrang=
es)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-ggplot2&quot; ,r-ggplot2=
)<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-iranges&quot; ,r-iranges)<=
br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-mvtnorm&quot; ,r-mvtnorm)<br=
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-reshape2&quot; ,r-reshape2)<br=
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-rsamtools&quot; ,r-rsamtools)<=
br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (&quot;r-s4vectors&quot; ,r-s4vectors=
)))<br>=C2=A0 =C2=A0 =C2=A0 (native-inputs `((&quot;r-knitr&quot; ,r-knitr)=
))<br>=C2=A0 =C2=A0 =C2=A0 (home-page<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 &quot;=
<a href=3D"https://git.bioconductor.org/packages/chromstaR">https://git.bio=
conductor.org/packages/chromstaR</a>&quot;)<br>=C2=A0 =C2=A0 =C2=A0 (synops=
is<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 &quot;Combinatorial and Differential Chro=
matin State Analysis for ChIP-Seq Data&quot;)<br>=C2=A0 =C2=A0 =C2=A0 (desc=
ription<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 &quot;This package implements functi=
ons for combinatorial and differential analysis of ChIP-seq data.=C2=A0 It =
includes uni- and multivariate peak-calling, export to genome browser viewa=
ble files, and functi<br>ons for enrichment analyses.&quot;)<br><div>=C2=A0=
 =C2=A0 =C2=A0 (license artistic2.0))))</div><div><br></div><div>with best =
regards,</div><div>Hong Li<br></div></div>

--0000000000001de91c05bdc47c1d--



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