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Author: TJonCooper

CITATION.cff

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+cff-version: 1.1.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: Frishberg
+    given-names: Amit
+  - family-names: Milman
+    given-names: Neta
+  - family-names: Alpert
+    given-names: Ayelet
+  - family-names: Alpert
+    given-names: Ayelet
+  - family-names: Spitzer
+    given-names: Hannah
+  - family-names: Asani
+    given-names: Ben
+  - family-names: Schiefelbein
+    given-names: Johannes B.
+  - family-names: Bakin
+    given-names: Evgeny
+  - family-names: Regev-Berman
+    given-names: Karen
+  - family-names: Priglinger
+    given-names: Siegfried G.
+  - family-names: Schultze
+    given-names: Joachim L.
+  - family-names: Theis
+    given-names: Fabian J.
+  - family-names: Shen-Orr
+    given-names: Shai S.
+title: Reconstructing disease dynamics for mechanistic insights and clinical benefit
+version: Official
+date-released: 2023-07-27

DESCRIPTION

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+Package: TimeAx
+Type: Package
+Title: Multiple trajectory alignment of time-series data
+Version: 0.1.1
+Author: Amit Frishberg [aut, cre],  Neta Milman [aut], Ayelet Alpert [aut], Joachim L. Schultze [aut], Fabian Theis [aut], Shai S. Shen-Orr [aut]
+Maintainer: Amit Frishberg <amfrishberg@gmail.com>
+URL: https://github.com/amitfrish/TimeAx
+BugReports: https://github.com/amitfrish/TimeAx/issues
+Description: TimeAx, a method that models disease dynamics over time based on time-series data from multiple individuals, thus tracing the dynamics and progression rates associated with molecular mechanisms of the disease and patients’ clinical outcomes. Similar to computational sequence alignment approaches, which provide biologists the capability to understand DNA and protein function through a quantitative comparison, TimeAx performs multiple alignment of shared dynamics across a common trajectory, thus allowing the modeling of any type of continuous process and its quantitative comparison.
+License: GPL-2
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.1.2
+biocViews: limma
+Depends: R (>= 4.1.0)
+Imports: dtw, foreach, parallel, doSNOW, phangorn, fields, Matrix, cppRouting, stats

LICENCE

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+MIT License
+
+Copyright (c) 2022 Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) and Technion-Israel Institute of Technology
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(detectSeed)
+export(modelCreation)
+export(predictByConsensus)
+export(robustness)
+importFrom("grDevices","chull")
+importFrom("stats","sd")
+importFrom("stats","var")
+importFrom("utils","setTxtProgressBar")