Author: Rebecka Jornsten, Tobias Abenius, Sven Nelander
Depends: R (>= 2.12.0), lassoshooting (>= 0.1.4), Matrix, methods, irr,

Depends: R (>= 2.10.0), lassoshooting (>= 0.1.3), Matrix, methods, irr,

Depends: R (>= 2.12.0), lassoshooting (>= 0.1.4), Matrix, methods,
Imports: irr, elasticnet, survival, Rgraphviz
Description: Estimates sparse matrices A or G using fast lasso regression from mRNA transcript levels Y and CNA profiles U. Two models are provided, EPoC A where
the matrices R and E are so far treated as noise. For details see the reference and the manual page of `lassoshooting'.

Title: Endogenous Perturbation Analysis of Cancer
Depends: R (>= 2.12.0), lassoshooting (>= 0.1.4), Matrix, methods
the matrices R and E are so far treated as noise. For
details see the manual page of 'lassoshooting' and the
article Rebecka Jörnsten, Tobias Abenius, Teresia Kling,
Linnéa Schmidt, Erik Johansson, Torbjörn E M Nordling,
Bodil Nordlander, Chris Sander, Peter Gennemark,
Keiko Funa, Björn Nilsson, Linda Lindahl, Sven Nelander

Title: Clinical Coding of Patients with Kidney Disease
Description: Clinical coding and diagnosis of patients with kidney using
clinical practice guidelines. The guidelines used are the evidence-based
KDIGO guidelines, see <https://kdigo.org/guidelines/> for more information.
This package covers acute kidney injury (AKI), anemia, and
tibble (>= 3.0.1), vctrs, ellipsis, rlang (>= 0.4.0), units (>=
Suggests: usethis, testthat, covr, knitr, rmarkdown
Author: Alwin Wang [aut, cre] (<https://orcid.org/0000-0003-4883-2917>),

ellipsis, rlang (>= 0.4.0), units (>= 0.7), lubridate (>=
Suggests: usethis, testthat, covr, knitr, rmarkdown, vctrs,

Description: Provides a set of functions, which facilitates removing objects from an environment.
It allows to delete objects specified with regular expression or with other conditions (e.g. if object is numeric),
Packaged: 2020-03-21 11:28:00 UTC; krzysztof

Description: Analysis and visualization of similarities between epilepsy ontologies based on text mining results by comparing ranked lists of co-occurring drug terms in the corpus of LIVIVO. The ranked result lists of neurological drug terms co-occurring with named entities from the epilepsy ontologies EpSO, ESSO, and EPILONT are aggregated in order to generate two different results: an overview table of drugs that are relevant to epilepsy created with the method createNeuroTable, and a plot of tanimoto similarity coefficients between the aggregated list of drug terms against the list of drug terms from each of the ontologies created with the method createTanimotoBaseline(). The alignment of the Top-K Ranked Lists is conducted using the R-package TopKLists <https://cran.r-project.org/package=TopKLists>. The source data to create the ranked lists of drug names is produced using the text mining workflows described in Mueller, Bernd and Hagelstein, Alexandra (2016) <doi:10.4126/FRL01-006408558> and Mueller, Bernd et al. (2017) <doi:10.1007/978-3-319-58694-6_22>.
Imports: hashmap, ggplot2, tidyr, dplyr, testthat, gridExtra,