NEWS.md

In ilyessr/conclus: ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion

Changes in version 0.99.343 (2021-04-09)

• Submission to Bioconductor

• NAMESPACE

• Imported BiocFileCache package and R_user_dir() of tools package

• Exported new function conclusCacheClear()

• DESCRIPTION

• Removed LazyData: true.

• DataFormatting.R

• Added a caching system for retrieveFromGEO()
• Created conclusCacheClear() to delete the cache

• Updated documentation

• loadDataset.R

• Updated documentation

• Simplified nested "if" in loadDataset.R

• methods-normalization.R

• Modified the use of getBM to retrieve only genes of the count matrix (instead of the all database)

• test_setters.R/test_getters.R

• Modified documentation for loadDataOrMatrix()

• Simplified nested "if" in loadDataset.R

• test_loadData.R

• Adapted the unit tests to the new format of coldata and rowdata

• test_scRNAseq-methods.R

• Changed the experiment name to "Light_Experience"

• Used tempdir() for output directory

• inst

• Added inst/script to generate data on inst/extdata

• New data generated

• vignette

• Used tempdir() for output directory
• Specified other parameters in the first example of runCONCLUS for the very small dataset
• Replaced old paths by new ones

Changes in version 1.1.002 (2021-08-31)

• Made the following significant changes
• Added an internal function .retrieveClustersNumberK to suggest the clusters number to use in lusterCellsInternal().
• Added suggestedClustersNumber slot in scRNAseq class to retrieve this suggested clusters number.
• Added accessors getSuggestedClustersNumber and setSuggestedClustersNumber.
• Updated all the objects used in examples and tests to have this slot.

Changes in version 1.3.4 (2022-03-28)

• Made the following significant changes
• Add parameter removeNoSymbol in the method normalizeCountMatrix to filter genes doesn't have SYMBOL.
• clusterMarkers slot become topMarkers slot, accessors names change in the same way.0

ilyessr/conclus documentation built on April 8, 2022, 1:43 p.m.