Title: Convert Counts to Fragments per Kilobase of Transcript per
Authors@R: c(person("Ahmed", "Alhendi", email = "asna4@le.ac.uk",role = c("aut","cre")))
Depends: R (>= 3.1.0), ComplexHeatmap, circlize, stats
Description: 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.

Title: Transform Counts in RNA-Seq Data Analysis
person("Minseok", "Seo", role = c("aut", "ctb"),
person("Craig P.", "Hersh", role = c("aut", "ctb"),
Description: 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>.

Description: 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. (2019) <doi.org/10.1038/s41598-019-41315-w>.

Title: Locates and Counts Pixels Within Color Range(s) in Images
Description: Counts colors within color range(s) in images, and
provides a masked version of the image with targeted pixels
changed to a different color. Output includes the locations
of the pixels in the images, and the proportion of the image
within the target color range with optional background masking.
Users can specify multiple color ranges for masking.
Imports: colordistance, tools, graphics, png, jpeg

Title: The Beta-Binomial Test for Count Data
Authors@R: c(person("Thang", "Pham", email = "t.pham@amsterdamumc.nl",
Description: The beta-binomial test is used for significance analysis of independent samples by Pham et al. (2010) <doi:10.1093/bioinformatics/btp677>. The inverted beta-binomial test is used for paired sample testing, e.g. pre-treatment and post-treatment data, by Pham and Jimenez (2012) <doi:10.1093/bioinformatics/bts394>.