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.github/ISSUE_TEMPLATE/question.md

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assignees: ''
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---
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.github/workflows/deploy.yml

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- name: Install pypa/build
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run: >-
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cd python &&
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cd python &&
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python -m
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pip install
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build

LICENSE

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consider it more useful to permit linking proprietary applications with the
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library. If this is what you want to do, use the GNU Lesser General
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Public License instead of this License.
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README.md

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MAGIC has been implemented in Python, Matlab, and R.
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#### To get started immediately, check out our tutorials:
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##### Python
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* [Epithelial-to-Mesenchymal Transition Tutorial](http://nbviewer.jupyter.org/github/KrishnaswamyLab/MAGIC/blob/master/python/tutorial_notebooks/emt_tutorial.ipynb)
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* [Bone Marrow Tutorial](http://nbviewer.jupyter.org/github/KrishnaswamyLab/MAGIC/blob/master/python/tutorial_notebooks/bonemarrow_tutorial.ipynb)
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##### R
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* [Epithelial-to-Mesenchymal Transition Tutorial](http://htmlpreview.github.io/?https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/emt_tutorial.html)
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* [Bone Marrow Tutorial](http://htmlpreview.github.io/?https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/bonemarrow_tutorial.html)
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#### To get started immediately, check out our tutorials:
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##### Python
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* [Epithelial-to-Mesenchymal Transition Tutorial](http://nbviewer.jupyter.org/github/KrishnaswamyLab/MAGIC/blob/master/python/tutorial_notebooks/emt_tutorial.ipynb)
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* [Bone Marrow Tutorial](http://nbviewer.jupyter.org/github/KrishnaswamyLab/MAGIC/blob/master/python/tutorial_notebooks/bonemarrow_tutorial.ipynb)
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##### R
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* [Epithelial-to-Mesenchymal Transition Tutorial](http://htmlpreview.github.io/?https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/emt_tutorial.html)
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* [Bone Marrow Tutorial](http://htmlpreview.github.io/?https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/bonemarrow_tutorial.html)
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<p align="center">

Rmagic/DESCRIPTION

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Title: MAGIC - Markov Affinity-Based Graph Imputation of Cells
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Version: 2.0.3.999
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Authors@R: c(person(given = "David", family = "van Dijk", email = "[email protected]", role = c("aut")),
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person(given = 'Scott', family = 'Gigante', email = '[email protected]', role = 'cre',
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person(given = 'Scott', family = 'Gigante', email = '[email protected]', role = 'cre',
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comment = c(ORCID = '0000-0002-4544-2764')))
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Maintainer: Scott Gigante <[email protected]>
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Description: MAGIC (Markov affinity-based graph imputation of cells) is a method for addressing technical noise in single-cell data, including under-sampling of mRNA molecules, often termed "dropout" which can severely obscure important gene-gene relationships. MAGIC shares information across similar cells, via data diffusion, to denoise the cell count matrix and fill in missing transcripts. Read more: van Dijk et al. (2018) <DOI:10.1016/j.cell.2018.05.061>.

Rmagic/LICENSE

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consider it more useful to permit linking proprietary applications with the
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library. If this is what you want to do, use the GNU Lesser General
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Public License instead of this License.
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Rmagic/R/magic_testdata.R

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#' @format A matrix with 500 rows and 197 variables
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#'
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#' @source The authors
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"magic_testdata"
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"magic_testdata"

Rmagic/R/utils.R

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}
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#' Check whether MAGIC Python package is available and can be loaded
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#'
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#'
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#' This is used primarily to avoid running tests on CRAN
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#' and elsewhere where the Python package should not be
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#' installed.
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#'
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#'
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#' @export
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pymagic_is_available <- function() {
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tryCatch({

Rmagic/README.md

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library(viridis)
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#> Loading required package: viridisLite
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library(phateR)
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#>
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#>
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#> Attaching package: 'phateR'
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#> The following object is masked from 'package:Rmagic':
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#>
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#>
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#> library.size.normalize
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```
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Rmagic/inst/CITATION

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bibtype="Article",
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title="Recovering Gene Interactions from Single-Cell Data Using Data Diffusion",
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author = c(
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person("David", "van Dijk"),
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person("Roshan", "Sharma"),
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person("Juozas", "Nainys"),
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person("Kristina", "Yim"),
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person("Pooja", "Kathail"),
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person("Ambrose J.", "Carr"),
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person("Cassandra", "Burdziak"),
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person("Kevin R.", "Moon"),
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person("Christine L.", "Chaffer"),
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person("Diwakar", "Pattabiraman"),
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person("Brian", "Bierie"),
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person("Linas", "Mazutis"),
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person("Guy", "Wolf"),
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person("Smita", "Krishnaswamy"),
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person("David", "van Dijk"),
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person("Roshan", "Sharma"),
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person("Juozas", "Nainys"),
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person("Kristina", "Yim"),
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person("Pooja", "Kathail"),
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person("Ambrose J.", "Carr"),
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person("Cassandra", "Burdziak"),
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person("Kevin R.", "Moon"),
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person("Christine L.", "Chaffer"),
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person("Diwakar", "Pattabiraman"),
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person("Brian", "Bierie"),
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person("Linas", "Mazutis"),
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person("Guy", "Wolf"),
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person("Smita", "Krishnaswamy"),
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person("Dana", "Pe'er")),
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year=2018,
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url="https://www.cell.com/cell/abstract/S0092-8674(18)30724-4",

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