Changes in version 0.9.2 (2025-09-11)                  

    o   Fix issue with running multiNMF on a sigle sample

    o   Improved definition of cumulative weight for genes in MP

    o   Update category -> collection for runGSEA

    o   Replace deprecated 'slot' calls

    o   Easier implementation for custom annotation colors (as named
	vectors)

                 Changes in version 0.8.0 (2025-04-24)                  

    o   Compatibility with RcppML >= 0.5.6 (currently not on CRAN)

                        Changes in version 0.7.0                        

    o   The function 'getMetaPrograms()' now returns also a matrix of
	"metaprogram composition", in terms of how many individual
	programs from each sample contributed to defining the MP. This
	is stored in the 'metaprograms.composition' slot of the
	resulting object

    o   The function 'runGSEA()' now allows running gene set enrichment
	against a custom DB of signatures

    o   Check that parameter 'k' is an integer >=2

                 Changes in version 0.6.2 (2024-11-12)                  

    o   Automatic downsample of the gene program similarity heatmap
	(plotMetaPrograms() function). It avoids overloading the
	graphics device when running GeneNMF with many samples. See the
	'downsample' parameter in plotMetaPrograms().

    o   New function 'dropMetaPrograms()' to remove MPs from GeneNMF
	results.

                 Changes in version 0.6.0 (2024-07-22)                  

    o   We updated how meta-programs (MPs) are calculated from
	individual programs. Instead of extracting gene sets for each
	program and then calculating a consensus, we keep the full
	vector of gene weights and calculate cosine similarities
	between the vectors. Consensus gene weights are then calculated
	as the average over all programs in a MP.

    o   To impose sparsity in the decomposition, we include a
	`specificity.weight` parameter, which is used to re-normalize
	NMF loadings based on how specific a gene is for a given
	program.

    o   To determine the number of genes to be included in a MP, we
	calculate the cumulative distribution for the gene weights in a
	given MP. Only genes that cumulatively explain up to a fraction
	of the total weight (`weight.explained` parameter) are included
	in the MP gene set.

    o   The definition and default of `min.confidence` has changed. The
	confidence of a gene in a given MP is calculated as the
	fraction of programs in which the gene has been determined to
	be part of the invidual program (using `weight.explained=0.8`).

    o   The parameter `nprograms` in the function `getMetaPrograms()`
	has been renamed to `nMP`, to avoid confusion

    o   New defaults: expression matrices are now by default not scaled
	or centered (the behavior can be altered using the `scale` and
	`center` parameters)

                 Changes in version 0.4.0 (2024-02-29)                  

    o   First stable version