Implements cointegration/cotrending rank selection
algorithm in Guo and Shintani(2011). Paper: "Consistant
Cotrending rank selection when both stochastic and nonlinear
deterministic trends are present", Preprint, Feb 2011.

R (>= 3.0.0), RCurl, bitops, httr, rjson
couchDB instance to connect to and work on.

Connect to and Work with CouchDB Databases
Interface to the couchDB document database <http://couchdb.apache.org>.
c(person("Aleksander", "Dietrichson", ,
"sasha@xrrch.com",
c("aut", "cre")),
person("Frans", "van Dunn<c3><a9>", ,
"frans@ixpantia.com",
c("ctb"))
)
couchDB instance to connect to and work with.
Aleksander Dietrichson [aut, cre],
Frans van Dunn<c3><a9> [ctb]

Penalized Estimation of Flexible Hidden Markov Models for Time
Series of Counts
Provides tools for penalized estimation of flexible hidden Markov models for time series of counts w/o the need to specify a (parametric) family of distributions. These include functions for model fitting, model checking, and state decoding. For details, see Adam, T., Langrock, R., and Weiß, C.H. (2019): Penalized Estimation of Flexible Hidden Markov Models for Time Series of Counts. <arXiv:1901.03275>.

Convert Counts to Fragments per Kilobase of Transcript per
Million (FPKM)
c(person("Ahmed", "Alhendi", email = "asna4@le.ac.uk",role = c("aut","cre")))
R (>= 3.1.0), ComplexHeatmap, circlize, stats
Implements the algorithm described in Trapnell,C. et al. (2010) <doi: 10.1038/nbt.1621>. This function takes read counts matrix of RNA-Seq data, feature lengths which can be retrieved using 'biomaRt' package, and the mean fragment lengths which can be calculated using the 'CollectInsertSizeMetrics(Picard)' tool. It then returns a matrix of FPKM normalised data by library size and feature effective length. It also provides the user with a quick and reliable function to generate FPKM heatmap plot of the highly variable features in RNA-Seq dataset.

Transform Counts in RNA-Seq Data Analysis
c(
person("Zeyu", "Zhang", role=c("aut", "cre"),
email = "zhzyvv@gmail.com"),
person("Danyang", "Yu", role=c("aut", "ctb"),
email = "YuDanyang1995@outlook.com"),
person("Minseok", "Seo", role = c("aut", "ctb"),
email = "minseok.seo@channing.harvard.edu"),
person("Craig P.", "Hersh", role = c("aut", "ctb"),
email = "craig.hersh@channing.harvard.edu"),
person("Scott T.", "Weiss", role = c("aut", "ctb"),
email = "scott.weiss@channing.harvard.edu"),
person("Weiliang", "Qiu", role=c("aut", "ctb"),
email = "weiliang.qiu@gmail.com")
)
Provide data transformation functions to transform counts in RNA-seq data analysis. Please see the reference: Zhang Z, Yu D, Seo M, Hersh CP, Weiss ST, Qiu W. (2018) <doi:10.1101/432690>.
Zeyu Zhang [aut, cre],
Danyang Yu [aut, ctb],
Minseok Seo [aut, ctb],
Craig P. Hersh [aut, ctb],
Scott T. Weiss [aut, ctb],
Weiliang Qiu [aut, ctb]