Differential analyses and Enrichment pipeline for bulk 'ATAC-seq' data
analyses. This package combines different packages to have an ultimate package
for both data analyses and visualization of 'ATAC-seq' data. Methods are described in
Karakaslar et al. (2021) <doi:10.1101/2021.03.05.434143>.

Differential analyses and Enrichment pipeline for bulk 'ATAC-seq' data
analyses. This package combines different packages to have an ultimate package
for both data analyses and visualization of 'ATAC-seq' data. Methods are described in
'Karakaslar et al.' (2021) <doi:10.1101/2021.03.05.434143>.
ChIPseeker, DESeq2, dplyr, edgeR, fgsea, GenomicRanges,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, ggplot2, ggrepel,
grDevices, limma, utils, pheatmap, preprocessCore,
RColorBrewer, sva, writexl

Ready-to-Use Curated Gene Sets for 'cinaR'
Immune related gene sets provided along with the 'cinaR' package.

Simple interpolation methods designed to be used from C
code. Supports constant, linear and spline interpolation. An R
wrapper is included but this package is primarily designed to be
used from C code using 'LinkingTo'.  The spline calculations are
classical cubic interpolation, e.g., Forsythe, Malcolm and Moler
(1977) <ISBN: 9780131653320>.
person("Rich", "FitzJohn", role = c("aut", "cre"),
email = "rich.fitzjohn@gmail.com")

Encryption and Decryption with Text Ciphers
person("Gus", "Lipkin", , "gus.lipkin@gmail.com", role = c("aut", "cre"))
Encrypts and decrypts using basic ciphers. None of
these should be used in place of real encryption using state of the art tools.
The ciphers included use methods described in the ciphers's Wikipedia and
cryptography hobby websites.

Nonparametric estimation of monotone functions via isotonic regression and centered isotonic regression
The 'cir' package provides a documented version of the well-known isotonic regression (IR) algorithm (function 'pava'), and an improvement to IR in case the true function is known to be smooth and strictly monotone. This improvement called Centered Isotonic Regression (CIR) is available via the function 'cir.pava'. Additionally, the function 'cir.upndown' provides percentile estimation for dose-response experiments (e.g., ED50 estimation of a medication) using CIR.