dsb v1.0.4

dsb v1.0.4 is now on CRAN: https://cran.r-project.org/package=dsb
This is a patch to update documentation and integrate a PR.
For more details on updates please see news.md file: https://github.com/niaid/dsb/blob/master/NEWS.md

dsb v1.0.3

dsb v1.0.3 is on CRAN: https://cran.r-project.org/package=dsb
This is a patch to address a CRAN check with no function updates.
For more details on updates please see news.md file: https://github.com/niaid/dsb/blob/master/NEWS.md

dsb v1.0.2

dsb v1.0.2 is on CRAN: https://cran.r-project.org/package=dsb

For more details on updates please see news.md file for release: https://github.com/niaid/dsb/blob/master/NEWS.md

dsb v1.0.1

dsb v1.0.1 is now on CRAN: https://cran.r-project.org/package=dsb

For more details on updates please see news.md file for release 1.0.1: https://github.com/niaid/dsb/blob/master/NEWS.md

• 3 new vignettes added.
• New function ModelNegativeADTnorm for normalizing ADTs without using empty droplets.
• Feature complete version of the package referenced in forthcoming publication.
  This release is a patch for 1.0.0 released earlier today that fixed a markdown rendering issue in v1.0.0.

dsb v1.0.0

dsb v1.0.0 is now on CRAN: https://cran.r-project.org/package=dsb

For more details on updates please see news.md file for release 1.0.0: https://github.com/niaid/dsb/blob/master/NEWS.md

• Feature complete version of the package referenced in forthcoming publication.
• 3 new vignettes added.
• New function for modeling background and normalizing ADTs without using empty droplets added.
• Note the main vignette is not properly rendering on CRAN so the old version of the vignette is shown, please use the github readme for now. This issue will be fixed shortly with a v1.0.1 patch.

dsb v0.3.0

dsd v0.3.0 is now on CRAN: https://CRAN.R-project.org/package=dsb

Additional input data checking added. Additional internal statistics used by dsb can also be returned if requested by user.

For more details on updates please see news.md file for release 0.3.0: https://github.com/niaid/dsb/blob/master/NEWS.md

dsb v0.2.0

dsb 0.2.0

dsb 0.2.0 is now on CRAN https://cran.r-project.org/package=dsb

Enhancements

Return dsb internal stats

Some advanced users may desire to look into the latent noise variables estimated by dsb. Setting return.stats = TRUE now returns a list, the first element is the dsb normalized ADT values, the second element is a dataframe of noise variables for each cell, including the derived "dsb technical component" along with its constituent variables, the background mean and the isotype control protein values for each cell.

quantile clipping

Rarely, a small minority of cells can have outlier values for a single protein, for example expression at level -25 after normalization. These values can now be clipped to be the lowest / highest quantile by default c(0.001, 0.9995). To use this feature set quantile.clipping = TRUE and quantile.clip to be a vector of lowest and highest quantile values to use; defaults to c(0.001, 0.9995).

Documentation

Documentation has been overhauled, the main vignette now includes simpler estimation of cells vs empty drops by using the EmptyDrops method that is now implemented by Cell Ranger by default. A workflow for multimodal (CITE-seq) single cell analysis using the dsb method for normalization is provided including loading raw data, quality control, clustering and multiple versions of the Seurat Weighted Nearest Neighbors joint mRNA and protein clustering method. Added to FAQ section in vignette.

CRAN release

dsb 0.1.0

• dsb is now hosted on CRAN: go to dsb on CRAN

• Documentation is improved from the beta release based on user feedback with a clearer workflow for defining and performing QC on background droplets and cells defined from raw protein UMI data. Additional code is added for integrating dsb with Seurat, Scanpy in Python, and Bioconductor's SingleCellExperiment class. Added an FAQ section based on user questions and a workflow for both multiplexing experiments or for non-multiplexing / single lane experiments. See the updated documentation on CRAN

• The current dsb package defaults are: denoise.counts = TRUE and use.isotype.control = TRUE. Isotype controls are not required for normalization. See package documentation.