NEWS.md

In jmw86069/salsa: Single-cell Amalgamation by Latent Semantic Analysis (SALSA)

salsa version 0.0.4.900

changes to R-shiny app

• Cell x-axis can be log-scaled.
• Fit method defaults to "mge" with goodness of fit "KS" for Frechet-Weibull distribution. The previous "mle" is available for comparison and testing.

changes to existing functions

• The fr_wei distribution functions qfr_wei, pfr_wei, dfr_wei have had the argument log=FALSE removed, under guidance of the fitdistrplus package vignette.

Todo

• evaluate alternative optimization functions, influenced by a blog post by one of the original authors: https://www.r-bloggers.com/why-optim-is-out-of-date/ who suggests considering the "optextras" R package on CRAN. Major benefit would be substantial speed improvement, and potential increase in robustness.

salsa version 0.0.3.900

minor fixes

• Reference to local debugging files were removed from R-shiny app.

salsa version 0.0.2.900

additions

• First prototype of R-shiny app for the nUMI per cell and gene threshold workflow.

salsa version 0.0.1.900

additions

• Added examples for several functions.
• Two example datasets are included to help illustrate the workflow, oz2_numi_per_cell and oz2_numi_per_gene.
• get_salsa_steps(), do_salsa_steps() and get_salsa_table() are the core workflow for determining the upper and lower bound for scRNA-seq barcode and gene values to use in downstream analyses.

changes to existing functions

• do_salsa_steps() uses memoise to cache result for distribution fit functions fitdist_fr() and fitdist_fr_wei().
• do_salsa_steps() accepts custom parameter boundaries for the Frechet-Weibull fit, in data.frame format as returned by params_fr_wei(). The recommended workflow is to generate a default data.frame from params_fr_wei(), modify its values, then pass it as an argument to do_salsa_steps().
• params_fr_wei() now accepts partial custom input, and replaces non-NA values for only the rows and columns supplied, making it easier to supply only certain custom parameters.

salsa version 0.0.0.900

• Initial package creation.

jmw86069/salsa documentation built on May 21, 2019, 10:31 a.m.