CHANGES IN VERSION ccImpute 1.6.1 ----------------------------------- + Performance Optimizations: o Significantly enhanced calculation speed for Pearson and Spearman correlation matrices, including weighted versions. o Leveraged the Irlba package for efficient truncated Singular Value Decomposition (SVD) computation. o Optimized imputation by limiting the number of singular components while maintaining accuracy of downstream analysis, with adjustable maximum limits based on dataset size. o Optimized the identification of dropout events. o Introduced a fast dropout calculation method based on non-zero expression value means, preserving imputation performance, and great improving runtime speed. o Replaced SIMLR with Tracy-Widom Bound for estimating k when not provided, resulting in faster calculations and improved empirical performance. + Expanded Functionality: o Added support for sparse matrices in dgCmatrix format, improving memory efficiency. + Documentation Enhancements: o Expanded the vignette with detailed guidance and practical examples for maximizing the package's value and computational speed. o Included comparative benchmarking against previous releases in the vignette, demonstrating the performance improvements. + Overall Impact: o The ccImpute package is now substantially faster and more efficient. o Users can expect a smoother experience with improved documentation and expanded functionality. CHANGES IN VERSION ccImpute 0.99.0: ----------------------------------- o The first version 0.99.0 is submitted to Bioconductor