NEWS

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decontX 1.11.2

• The decontX-package help page now has a Value section, which fixes a BiocCheck warning.
• Documentation is regenerated with roxygen2 8.1.0, and the Stan model exports with rstantools 2.7.1. Results don't change.

decontX 1.11.1

• decontX no longer depends on the celda package (ADR-0003 Stage 1). The one internal use of celda::normalizeCounts() (proportion normalization inside simulateContamination()) is replaced by the package's own fastNormProp routine, which produces identical results, and the example and vignette now plot cluster labels and marker-gene expression on the UMAP with scater::plotReducedDim() instead of celda's plotting functions. This drops celda (and its transitive dependencies) entirely and removes the R CMD check deprecation warnings that came from celda's masked, stale copy of decontX being invoked after library(celda) in the examples.
• The cell cluster initialization used by decontX() when z is not supplied (log-normalization, variable gene selection, PCA, and UMAP) has been migrated from scater/scuttle to the scrapper package, because scuttle deprecated logNormCounts()/normalizeCounts() in Bioconductor 3.24. This removes the deprecation warnings from R CMD check.
• Results of decontX() without z may differ slightly from previous versions (same workflow and parameters; different variable-gene criterion and UMAP implementation). A new legacyInit = TRUE argument reproduces the previous behavior; it requires the scater package (now in Suggests) and is kept for backwards compatibility for as long as the upstream functions remain available. Users supplying their own z are unaffected.
• With the default initialization, the UMAP step itself is deterministic even when seed = NULL (scrapper seeds it explicitly), but overall decontX() results with seed = NULL remain non-reproducible because the EM initialization is unseeded — set a seed for full reproducibility.
• The plotting functions (plotDecontXContamination(), plotDecontXMarkerPercentage(), plotDecontXMarkerExpression(), plotDensity(), plotBoxByCluster()) no longer use the deprecated ggplot2::aes_string() or trans = scale argument, which removes the ggplot2 deprecation warnings they emitted. decontX now requires ggplot2 (>= 3.5.0).
• plotDecontXMarkerPercentage() and plotDecontXMarkerExpression() now work when x is a dense or sparse matrix (they previously failed with a ggplot2 aesthetics error when the plot was drawn). The facets of plotDecontXMarkerExpression() now follow the order of groupClusters, matching the x-axis.
• decontPro() no longer draws 1000 unused samples from the variational posterior. Only the mean of the approximation is used, but the draws scaled with the number of ADTs x droplets and could take hundreds of GB of disk and memory on large datasets (#46). On a 50 x 400 test dataset the temporary file shrank from 444 MB to 2 MB and peak memory from 3.0 GB to 1.2 GB. Results are unchanged. rstan's "Pareto k diagnostic" warning is no longer shown: it is estimated from the draws and would always report Inf with the minimal number of draws now requested.

decontX 1.10.0

• No significant changes (Bioconductor 3.23 release).

decontX 1.8.0

• No significant changes (Bioconductor 3.22 release).

decontX 1.6.0

• No significant changes (Bioconductor 3.21 release). Includes the DecontPro changes released in 1.4.1 on the Bioconductor 3.20 branch.

decontX 1.4.1 (2025-02-16)

• decontPro() gained an ambient_counts argument, so an empty-droplet count matrix can be supplied to estimate the ambient contamination profile empirically instead of inferring it from the filtered droplets.
• Breaking: the first argument of decontPro() was renamed from object to filtered_counts for consistency with the new ambient_counts argument. Code that passed the count matrix by name (decontPro(object = x, ...)) must be updated; positional calls are unaffected.
• The estimated ambient contamination profile is now returned in the parameters element of the decontPro() output (p_est).
• Updated deprecated array syntax in the Stan model, fixed a C compiler warning in matrixSums, and corrected a deconPro typo in the DecontPro vignette.

decontX 1.4.0

• No significant changes (Bioconductor 3.20 release).

decontX 1.2.0

• No significant changes (Bioconductor 3.19 release).

decontX 1.0.0

• First Bioconductor release (Bioconductor 3.18), providing decontX() for ambient RNA decontamination of single-cell RNA-seq counts and decontPro() for single-cell protein expression (CITE-seq/TotalSeq) data.

decontX 0.99.5 (2023-10-19)

• First submission to Bioconductor after review.