update NEWS.rd

Author: stemangiola

inst/NEWS.rd

@@ -64,3 +64,42 @@
     \item Fix epic deconvolution when using DelayedMatrix
     \item Allow as_SummarizedExperiment with multiple columns identifiers for .sample and .feature
 }}
+
+\section{Changes in version 2.0.0, Bioconductor 3.19 Release}{
+\itemize{
+    \item Major refactoring to improve code maintainability and performance. This included the removal of all tbl methods in favor of SummarizedExperiment-based approaches.
+    \item Replace deprecated pipe operator \%>\% with native |> operator for improved readability
+    \item Refactor functions to use explicit function definitions instead of dplyr pipes
+    \item Remove deprecated \code{action} parameter from multiple functions
+    \item Remove deprecated \code{as_data_frame} function and clean up related code
+    \item Remove all tbl methods in favor of SummarizedExperiment-based approaches
+    \item Remove deprecated \code{.sample} and \code{.transcript} parameters from various methods
+    \item Deprecate \code{.transcript} parameter in \code{aggregate_duplicates} and introduce \code{feature} parameter
+    \item Add \code{feature_column} parameter to \code{deconvolve_cellularity} function
+    \item Add \code{keep_integer} functionality to \code{aggregate_duplicates}
+    \item Add \code{get_X_cibersort} function and update \code{deconvolve_cellularity} for improved reference handling
+    \item Add \code{scale_x_log10_reverse} and \code{scale_y_log10_reverse} functions for enhanced axis transformations
+    \item Add \code{formula_design} parameter to \code{identify_abundant} and \code{keep_abundant} methods
+    \item Add \code{minimum_count_per_million} parameter to abundance-related methods
+    \item Add \code{cores} parameter for dynamic specification of CPU cores during execution
+    \item Add comprehensive tests for various functions in the analysis pipeline
+    \item Add \code{filterByExpr} function and update methods to support \code{minimum_count_per_million}
+    \item Enhance \code{as_SummarizedExperiment} function and deprecate \code{test_stratification_cellularity}
+    \item Enhance parameter handling and deprecation warnings in abundance-related methods
+    \item Enhance gene enrichment and testing functions for improved robustness and clarity
+    \item Enhance \code{aggregate_duplicates} function to robustly handle numeric columns
+    \item Update core functions to utilize dynamic core detection
+    \item Update functions to use metadata instead of internals for better data handling
+    \item Update differential analysis functions and documentation
+    \item Update package dependencies and improve documentation
+    \item Update examples and documentation to utilize the airway dataset
+    \item Update vignettes to replace \code{.contrasts} with \code{contrasts} parameter
+    \item Update vignettes to replace tidyverse with specific dplyr, tidyr, tibble, and purrr libraries
+    \item Update README and documentation for clarity and completeness
+    \item Fix CHECK issues and improve package validation
+    \item Fix image paths in vignettes and README for better compatibility
+    \item Remove logo image inclusion from vignettes for cleaner presentation
+    \item Remove obsolete figures and streamline content
+    \item Remove deprecated warnings and redundant messages
+    \item Several bug fixes and optimizations
+}}