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addressing minor issues
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‎.Rbuildignore

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^Meta$
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(^|/)\.misty\.temp$
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(^|/)results$
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^vignettes/mistySeurat.Rmd$
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^LICENSE$

‎.gitignore

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.misty.temp
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results
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vignettes/breast_A_1
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vignettes/breast_A_1.tgz
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/doc/
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/Meta/
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vignettes/mistySeurat.Rmd

‎DESCRIPTION

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Package: mistyR
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Type: Package
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Title: Multiview Intercellular SpaTial modeling framework
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Version: 0.99.5
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Version: 0.99.6
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Authors@R: c(
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person(given = "Jovan",
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family = "Tanevski",
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biocViews: Software, BiomedicalInformatics, CellBiology, SystemsBiology,
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Regression, DecisionTree, SingleCell
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Depends: R (>= 4.0)
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License: GPL-3 + file LICENSE
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License: GPL-3
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Encoding: UTF-8
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LazyData: true
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VignetteBuilder: knitr
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Imports: assertthat, caret, deldir, digest, distances, dplyr, filelock,
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furrr (>= 0.2.0), ggplot2, magrittr, MASS, purrr, ranger, readr, rlang,

‎NEWS.md

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# mistyR 0.99.6
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- Minor revisions for bioc release.
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# mistyR 0.99.5
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- Remove Seurat vignette from package due to missing hdf5r binary for R 4.1 on CRAN for MacOS.

‎R/misty.R

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# performance
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if (sum(target.model[["performance.estimate"]] < 0) > 0) {
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warning(paste("Negative performance detected and replaced with 0 for target", target))
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warning.message <-
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paste("Negative performance detected and replaced with 0 for target",
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target)
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warning(warning.message)
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}
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performance.estimate <- target.model[["performance.estimate"]] %>%

‎README.md

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## Installation
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Install from GitHub using remotes:
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Install from Bioconductor:
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```r
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if(!requireNamespace("BiocManager", quietly = TRUE))
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install.packages("BiocManager")
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BiocManager::install("mistyR")
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```
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or install the latest version from GitHub with `remotes`:
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```r
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# install.packages("remotes")
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remotes::install_github("saezlab/mistyR")
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```
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mistyR is dependent on the following packages that are available from CRAN:
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assertthat, caret, deldir, digest, distances, dplyr, filelock, furrr, ggplot2,
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magrittr, MASS, purrr, ranger, readr, rlang, rlist, stats, stringr, tibble,
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tidyr, withr
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and mainly for the purpose of building the vignettes suggests BiocStyle, future, igraph, knitr, Matrix, progeny, rmarkdown, sctransform, SingleCellExperiment, SpatialExperiment and SummarizedExperiment from CRAN or Bioconductor.
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and mainly for the purpose of building the vignettes suggests
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BiocStyle, future, igraph, knitr, Matrix, progeny, rmarkdown, sctransform, SingleCellExperiment, SpatialExperiment and SummarizedExperiment
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from CRAN or Bioconductor.
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The installation of MISTy without any additional dependencies and building vignettes should take only seconds.
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The installation of mistyR without any additional dependencies and building vignettes should take only seconds.
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## Usage
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Start by reading `vignette("mistyR")` to learn how to run mistyR. To use mistyR with commonly used objects for spatial omics data see the [articles](https://saezlab.github.io/mistyR/articles/).
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Example pipelines and synthetic data for running mistyR are also available from [this repository](/articles/). To run mistyR on the provided synthetic data run the script synthetic_pipeline.R.
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Example pipelines and synthetic data for running mistyR are also available from [this repository](https://github.com/saezlab/misty_pipelines). To run mistyR on the provided synthetic data run the script synthetic_pipeline.R.
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## Citation
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If you use mistyR for your research please cite the [following publication](https://doi.org/10.1101/2020.05.08.084145):
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> Jovan Tanevski, Attila Gabor, Ricardo Omar Ramirez Flores, Denis Schapiro, Julio Saez-Rodriguez (2020). Explainable multi-view framework for dissecting inter-cellular signaling from highly multiplexed spatial data. *bioRxiv*. doi: [10.1101/2020.05.08.084145](https://doi.org/10.1101/2020.05.08.084145)
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> Jovan Tanevski, Attila Gabor, Ricardo Omar Ramirez Flores, Denis Schapiro, Julio Saez-Rodriguez (2020). Explainable multi-view framework for dissecting inter-cellular signaling from highly multiplexed spatial data. *bioRxiv*. doi: [10.1101/2020.05.08.084145](https://doi.org/10.1101/2020.05.08.084145)

‎docs/404.html

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‎docs/LICENSE-text.html

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‎docs/articles/index.html

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‎docs/authors.html

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‎docs/index.html

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‎docs/pkgdown.yml

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mistyR: mistyR.html
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mistySeurat: mistySeurat.html
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mistySpatialExperiment: mistySpatialExperiment.html
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last_built: 2021-05-05T07:45Z
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last_built: 2021-05-05T09:04Z
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urls:
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reference: https://saezlab.github.io/mistyR/reference
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article: https://saezlab.github.io/mistyR/articles

‎docs/reference/index.html

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‎vignettes/mistyR.Rmd

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[Online articles](https://saezlab.github.io/mistyR/articles/)
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## Publication {.unnumbered}
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## Publication {-}
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*`r format(citation("mistyR"), "textVersion")`*
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