NEWS.md

In scPCA: Sparse Contrastive Principal Component Analysis

Changes in version 0.99.0 (2019-09-13)

• Submitted to Bioconductor

Changes in version 1.1.2 (2020-01-08)

• Added hierarchical clustering options for clustering based cross-validation

Changes in version 1.1.5 (2020-01-18)

• Fixed issue with matrix normalization
• Misc. big fixes
• Improvements to code coverage

Changes in version 1.1.11 (2020-02-02)

• Added more SPCA algorithm options
• SPCA via variable projection
• Randomized SPCA via variable projection
• New vignette section comparing performance of SPCA algorithms
• Improvements to code coverage

Changes in version 1.1.12 (2020-04-21)

• Updated citations
• Fixed typos in documentation

Changes in version 1.1.14 (2020-04-26)

• Fixing broken link in an internal function documentation page.

Changes in version 1.1.15 (2020-06-02)

• Fixing travis CI settings

Changes in version 1.3.2 (2020-08-05)

• Updated scPCA function documentation
• Corrected pelling mistakes

Changes in version 1.3.3 (2020-08-08)

• The n_centers argument no longer matters when When the contrasts argument is of length 1 and the penalty term is set to 0.
• Users can now pass in their own cluster labels

Changes in version 1.3.4 (2020-08-12)

• Replaced calls to base::eigen by RSpectra::eigs_sym to speed up eigendecompositions of contrastive covariance matrices. cPCA is now performed much more quickly when only whishing to compute a handful of leading contrastive principal components.
• Replaced calls to stats::cov by coop::covar to speed up computation of large sample covariance matrices.
• In future updates, we'd like to explore using the DelayedArray framework to support the analysis of larger datasets.

Changes in version 1.3.5 (2020-08-18)

• Fixed citations in docs
• Provided more detailed warning when RSpectra::eigs_sym fails to converge
• Included argumetns in scPCA to control RSpectra::eigs_sym convergence: error tolerance and max number of iterations

Changes in version 1.3.6 (2020-08-30)

• Fixed issue where n_centers was required when only one penalty and contrast term were provided
• Users can now pass factors and character vectors to the clusters argument.

Changes in version 1.3.7 and 1.3.8 (2020-09-01)

• Minor bug fixes

Changes in version 1.3.9 (2020-10-12)

• scPCA now accepts DelayedMatrix objects as target and background datasets.

Changes in version 1.3.10 (2020-10-16)

• Implementing suggested improvements from Aaron Lun

scPCA documentation built on Nov. 8, 2020, 6 p.m.