Updated website to reflect recent contributions

[LotharukpongJS]

Updated website to reflect recent contributions and improved the PlotSignatureTransformed() documentation.

Transformation parameter in PlotSignatureTransformed() Further information added about the transformations that can be assessed.

#' @param transforms a character vector of any valid function that transforms gene expression levels. Available options are:
#'  \itemize{
#' \item \code{transforms = "none"} : No transformation (absolute expression)
#' \item \code{transforms = "log2"} : Computes binary (i.e., base 2) logarithms, \eqn{log_{2}{X}}.
#' \item \code{transforms = "log"} : Computes natural logarithms, \eqn{log_{e}{X}}.
#' \item \code{transforms = "log10"} : Computes common logarithms (i.e., base 10), \eqn{log_{10}{X}}.
#' \item \code{transforms = "sqrt"} : Computes the (principle) square root, \eqn{\sqrt{X}}.
#' \item \code{transforms = "vst"} :  (Quickly) estimates dispersion trend and applies a variance stabilizing transformation (please make sure that the \pkg{DESeq2} package is installed).
#' \item \code{transforms = "rlog"} : (Robustly) estimates dispersion trend and applies a variance stabilizing transformation (please make sure that the \pkg{DESeq2} package is installed).
#' \item \code{transforms = "rank"} : Ranks genes from lowest to highest based on their expression levels, at each condition (e.g., developmental stage). The gene's expression value is replaced by its sample rank or average ranks in case of ties.
#' \item \code{transforms = "squared"}: Computes the square, \eqn{X^2}.
#' }

Update to NEWS.md Recent changes are now documented.

myTAI 1.0.1.9000
===========
## New Functions
- New function `PlotSignatureTransformed()` : Plot evolutionary signatures across transcriptomes and RNA-seq transformations
- New function `tfStability()`: Perform Permutation Tests Under Different Transformations (to test the robustness of the p-values of a given test (e.g. `FlatLineTest()`, `ReductiveHourglassTest()`, `ReverseHourglassTest()`, `EarlyConservationTest()` and `LateConservationTest()`) to expression data transformations)
- New function `LateConservationTest()` : Perform Reductive Late Conservation Test (to test for a high-mid-low (or high-high-low) TAI or TDI pattern)
- New function `lcScore()` : Compute the Hourglass Score for the LateConservationTest

## New Features
- `PlotSignature()` updated to be able to perform the `TestStatistic = "LateConservationTest"`.
- `PlotSignature()` now prints p-value as a subtitle rather than via `ggplot2::annotate()`.
- `tf()` now has a `pseudocount` parameter, which is useful for performing logarithmic transformations when there are genes with 0 counts.
- `tf()` now supports `vst` and `rlog` transformations from [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
- `tf()` now has an `intergerise` parameter, which is needed when applying `vst` or `rlog` transformations.
- `tf()` updated documentation for performing rank transformation, which assigns ranks to the gene expression values within each stage, based on their relative positions compared to other values.
- Improvements to existing test functions (`ecScore()`, `rhScore()` and `reversehourglassScore()`) to give a message when the phylotranscriptomic pattern is unlikely to follow the test statistics.

## Bug and Issue Fixes
- Some changes to remove errors and warnings from `devtools::test()` and `devtools::check()`, when building this package, which has been accumulated from previous updates.

Update to authors list As per request, I added myself and Nikola as author and contributor. This reflects recent contributions. As of today: LotharukpongJS 52 commits 43,882 ++ 20,689 -- lavakin 14 commits 464 ++ 474 --

I should add, however, that the number of contributions from my part is biased by the number of changes documented when updating the site through pkgdown::build_site().

[LotharukpongJS]

I still notice that the home site still doesn't contain images https://drostlab.github.io/myTAI/. I will have a look at this later.

[HajkD]

Hi @LotharukpongJS

Looks excellent and welcome to you and @lavakin to the core developer team of myTAI :)

With many thanks and very best wishes, Hajk

[HajkD]

Having the docs updated would be wonderful as well!