File R-singleCellHaystack.spec of Package R-singleCellHaystack
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# Spec file for package singleCellHaystack
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%global packname singleCellHaystack
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 1.0.2
Release: 0
Summary: A Universal Differential Expression Prediction Tool for Single-Cell and Spatial Genomics Data
Group: Development/Libraries/Other
License: MIT + file LICENSE
URL: http://cran.r-project.org/web/packages/%{packname}
Source: singleCellHaystack_1.0.2.tar.gz
Requires: R-base
Requires: R-ggplot2
Requires: R-reshape2
Requires: R-cli
Requires: R-glue
Requires: R-gtable
Requires: R-isoband
Requires: R-lifecycle
Requires: R-rlang
Requires: R-scales
Requires: R-tibble
Requires: R-vctrs
Requires: R-withr
Requires: R-plyr
Requires: R-Rcpp
Requires: R-stringr
Requires: R-farver
Requires: R-labeling
Requires: R-R6
Requires: R-RColorBrewer
Requires: R-viridisLite
Requires: R-magrittr
Requires: R-stringi
Requires: R-pillar
Requires: R-pkgconfig
Requires: R-utf8
# %%if 0%%{?sle_version} > 120400 || 0%%{?is_opensuse}
# # Three others commonly needed
# BuildRequires: tex(ae.sty)
# BuildRequires: tex(fancyvrb.sty)
# BuildRequires: tex(inconsolata.sty)
# BuildRequires: tex(natbib.sty)
# %else
# BuildRequires: texlive
# %endif
# BuildRequires: texinfo
BuildRequires: fdupes
BuildRequires: R-base
BuildRequires: R-ggplot2
BuildRequires: R-reshape2
BuildRequires: R-cli
BuildRequires: R-glue
BuildRequires: R-gtable
BuildRequires: R-isoband
BuildRequires: R-lifecycle
BuildRequires: R-rlang
BuildRequires: R-scales
BuildRequires: R-tibble
BuildRequires: R-vctrs
BuildRequires: R-withr
BuildRequires: R-plyr
BuildRequires: R-Rcpp-devel
BuildRequires: R-stringr
BuildRequires: R-farver
BuildRequires: R-labeling
BuildRequires: R-R6
BuildRequires: R-RColorBrewer
BuildRequires: R-viridisLite
BuildRequires: R-magrittr
BuildRequires: R-stringi
BuildRequires: R-pillar
BuildRequires: R-pkgconfig
BuildRequires: R-utf8
Suggests: R-knitr
Suggests: R-rmarkdown
Suggests: R-testthat
Suggests: R-SummarizedExperiment
Suggests: R-SingleCellExperiment
Suggests: R-SeuratObject
Suggests: R-cowplot
Suggests: R-wrswoR
Suggests: R-sparseMatrixStats
Suggests: R-ComplexHeatmap
Suggests: R-patchwork
%description
One key exploratory analysis step in single-cell genomics data analysis
is the prediction of features with different activity levels. For
example, we want to predict differentially expressed genes (DEGs) in
single-cell RNA-seq data, spatial DEGs in spatial transcriptomics data,
or differentially accessible regions (DARs) in single-cell ATAC-seq
data. 'singleCellHaystack' predicts differentially active features in
single cell omics datasets without relying on the clustering of cells
into arbitrary clusters. 'singleCellHaystack' uses Kullback-Leibler
divergence to find features (e.g., genes, genomic regions, etc) that
are active in subsets of cells that are non-randomly positioned inside
an input space (such as 1D trajectories, 2D tissue sections,
multi-dimensional embeddings, etc). For the theoretical background of
'singleCellHaystack' we refer to our original paper Vandenbon and Diez
(Nature Communications, 2020) <doi:10.1038/s41467-020-17900-3> and our
update Vandenbon and Diez (Scientific Reports, 2023)
<doi:10.1038/s41598-023-38965-2>.
%prep
%setup -q -c -n %{packname}
# the next line is needed, because we build without --clean in between two packages
rm -rf ~/.R
%build
%install
mkdir -p %{buildroot}%{rlibdir}
%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname}
test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
rm -f %{buildroot}%{rlibdir}/R.css
%fdupes -s %{buildroot}%{rlibdir}
#%%check
#%%{_bindir}/R CMD check %%{packname}
%files
%dir %{rlibdir}/%{packname}
%{rlibdir}/%{packname}/CITATION
%doc %{rlibdir}/%{packname}/DESCRIPTION
%{rlibdir}/%{packname}/INDEX
%license %{rlibdir}/%{packname}/LICENSE
%{rlibdir}/%{packname}/Meta
%{rlibdir}/%{packname}/NAMESPACE
%doc %{rlibdir}/%{packname}/NEWS.md
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/data
%{rlibdir}/%{packname}/doc
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%changelog
