Karen

1.0

Kalman Reaction Networks

0packages depend

2.3Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Luca Del CoreFirst published 2022-09-151 releasesCRAN page ↗

This is a stochastic framework that combines biochemical reaction networks with extended Kalman filter and Rauch-Tung-Striebel smoothing. This framework allows to investigate the dynamics of cell differentiation from high-dimensional clonal tracking data subject to measurement noise, false negative errors, and systematically unobserved cell types. Our tool can provide statistical support to biologists in gene therapy clonal tracking studies for a deeper understanding of clonal reconstitution dynamics. Further details on the methods can be found in L. Del Core et al., (2022) doi:10.1101/2022.07.08.499353.

Install

R (CRAN)Ubuntu (r2u)openSUSE (OBS)

install.packages("Karen", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-karen

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-Karen

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 2.7 min · r-oldrel-windows-x86_64

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

2.3K

CRAN downloads in the past year

Rank #18,907 · ~6/day · ~188/mo

Karen Releases R versions

Daily download trend is not available in this view yet.

19530 days

60990 days

2.3K1 year

Compare downloads with other packages →

Also on96 r2u30 autocran

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (14)

Matrixparallelgaussquadsplinesscales mvtnorm tmvtnormMASSigraph xtable stringr abind expmmethods

LinkingTo (0)

none

Suggests (1)

R.rsp

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Luca Del Core

Author, Maintainer, Copyright holder

Authors (4)

Luca Del Core

Author, Maintainer, Copyright holder

Marco Grzegorczyk

Author, Thesis advisor

Danilo Pellin

Author

Ernst Wit

Author, Thesis advisor

Luca Del Core

Author, Maintainer, Copyright holder

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2022-09-15
Total releases: 1 / 4 yrs
License: GPL-3 OSI
Download size: 572 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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