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DESCRIPTION
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DESCRIPTION
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Package: conos
Title: Clustering on Network of Samples
Version: 1.5.2
Authors@R: c(person("Viktor","Petukhov", email="[email protected]", role="aut"), person("Nikolas","Barkas", email="[email protected]", role="aut"), person("Peter", "Kharchenko", email = "[email protected]", role = "aut"), person("Weiliang", "Qiu", email = "[email protected]", role = c("ctb")), person("Evan", "Biederstedt", email="[email protected]", role=c("aut", "cre")))
Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
License: GPL-3
Copyright: See the file COPYRIGHTS for various conos copyright details
Encoding: UTF-8
LazyData: true
Depends:
R (>= 3.5.0), Matrix, igraph
biocViews:
Imports:
abind,
cowplot,
ComplexHeatmap,
dendextend,
dplyr,
ggplot2,
ggrepel,
gridExtra,
irlba,
leidenAlg,
magrittr,
methods,
N2R,
parallel,
R6,
reshape2,
rlang,
Rtsne,
sccore (>= 1.0.0),
stats,
tools,
utils
RoxygenNote: 7.2.3
Suggests:
AnnotationDbi,
BiocParallel,
conosPanel,
drat,
DESeq2,
entropy,
ggrastr,
GO.db,
jsonlite,
knitr,
org.Hs.eg.db,
org.Mm.eg.db,
p2data,
pagoda2,
PMA,
plyr,
rhdf5,
rmarkdown,
rmumps,
Seurat,
shinycssloaders,
SummarizedExperiment,
testthat,
tibble,
uwot,
zoo
Additional_repositories: https://kharchenkolab.github.io/drat/
URL: https://github.com/kharchenkolab/conos
BugReports: https://github.com/kharchenkolab/conos/issues
NeedsCompilation: yes
LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppProgress
Author: Viktor Petukhov [aut], Nikolas Barkas [aut], Peter Kharchenko [aut], Weiliang Qiu [ctb], Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <[email protected]>