testthat, ggplot2, future.apply, future, knitr

testthat, ggplot2, future.apply, future, knitr, markdown

Disk-based implementation of
Functional Pruning Optimal Partitioning with up-down constraints
<doi:10.18637/jss.v101.i10> for single-sample peak calling
(independently for each sample and genomic problem),
can handle huge data sets (10^7 or more).

Joint Peak Detection in Several ChIP-Seq Samples
Jointly segment several ChIP-seq samples to find the peaks
which are the same and different across samples. The fast approximate
maximum Poisson likelihood algorithm is described in
"PeakSegJoint: fast supervised peak detection via joint segmentation
of multiple count data samples"
<arXiv:1506.01286> by TD Hocking and G Bourque.
data.table (>= 1.9.4), PeakError, parallel, penaltyLearning

testthat, ggplot2 (>= 2.0), microbenchmark

Optimal Segmentation Subject to Up-Down Constraints
Computes optimal changepoint models using the
Poisson likelihood for non-negative count data,
subject to the PeakSeg constraint:
the first change must be up, second change down, third change up, etc.
For more info about the models and algorithms,
read "A log-linear time algorithm for constrained changepoint detection"
<arXiv:1703.03352> by TD Hocking et al.
PeakSegDP (>= 2016.08.06), ggplot2, testthat, data.table (>=
1.9.8)

Spectrum manipulation: background estimation, Markov
smoothing, deconvolution and peaks search functions. Ported
from ROOT/TSpectrum class.

Implementation of the Pearson distribution system,
including full support for the (d,p,q,r)-family of functions
for probability distributions and fitting via method of moments
and maximum likelihood method.

Implementation of the Pearson distribution system, including full
support for the (d,p,q,r)-family of functions for probability distributions
and fitting via method of moments and maximum likelihood method.

c(person("Martin","Becker", role = c("aut","cre"),
email = "martin.becker@mx.uni-saarland.de"),
person("Stefan","Klößner", role = c("aut"),
email = "S.Kloessner@mx.uni-saarland.de"))
Martin Becker [aut, cre],
Stefan Klößner [aut]