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sccore

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R package sccore by kharchenkolab — release notes from GitHub.

github.com/kharchenkolab/sccore ↗

Shared plumbing for the Kharchenko single-cell stack, updated once a year

single-cellbioinformaticsr-packagecran-complianceinteroperability
◆Current state
sccore is the utility layer under the Kharchenko lab's single-cell packages — embedding plots, dot plots, parallel apply helpers and distance metrics that the downstream tools depend on rather than a tool researchers drive directly. The recent releases fix the Jensen-Shannon distance computation between matrix columns and add optional OpenMP support to the RcppArmadillo build. Cadence is roughly one CRAN release a year.
◆Where it's heading
Work splits cleanly into two streams: keeping the compiled build acceptable to CRAN as its Makevars policy shifts, and small correctness or interoperability fixes to the plotting and distance helpers. The interoperability thread is the one with direction — embeddingPlot() learning to read Seurat objects in 1.0.6 points at meeting users in the dominant single-cell framework rather than requiring the lab's own object types.
◆Prediction
Expect the next release to be driven by a CRAN toolchain requirement or a downstream package's needs, with any user-facing change likely another interoperability or plotting fix rather than new capability.

◆Recent moves

  1. 4mo ago

    Jensen-Shannon distance fixed, OpenMP support added

    jsDist() is corrected to compute the Jensen-Shannon distance between matrix columns accurately — a numerical fix that propagates to anything downstream using it for cell-cell or cluster comparison. OpenMP is enabled for RcppArmadillo where available, and the obsolete Rcpp:::LdFlags() call is dropped per CRAN.

    View source ↗
  2. 1y ago

    embeddingPlot() reads Seurat objects directly

    embeddingPlot() now accepts Seurat objects and works with their metadata and reductions, removing a conversion step for the majority of single-cell users who live in Seurat. The most direction-carrying change in the recent history of an otherwise maintenance-driven package.

    View source ↗
  3. 2y ago

    Version 1.0.5

    Build-only changes: /usr/lib linking removed from the Makevars files along with unnecessary pthread, stdc++ and libm flags. No user-visible effect.

    View source ↗
  4. 3y ago

    Version 1.0.4

    A scale.center argument is added to dotPlot() so average expression levels plot correctly. Small, but it changes what a commonly used figure actually shows.

    View source ↗
  5. 3y ago

    Version 1.0.3

    Adds checkPackageInstalled and saveDeAsJson helpers plus a dotPlot bugfix, alongside the C++11 declaration cleanup CRAN required. The JSON export helper is the piece downstream tools can build on.

    View source ↗
  6. 3y ago

    Version 1.0.2

    HTML5 validation fixes requested by CRAN for R 4.2.0, a few class() conditionals removed, and plapply() defaulting to mc.allow.recursive = TRUE. Compliance work with negligible user-facing surface.

    View source ↗