Changelog

Source: NEWS.md

scMerge 1.1.6

  • Accepts DelayedArray, HDF5Array and dgCMatrix inputs in the slots of input SCE objects.
  • Significant speed optimisation on scSEGIndex and add BiocParallel support.
  • Updated scSEGIndex references after publication.
  • scMerge now has the svd_k input that controls the number eigenvectors needed in the RUV step to allow fast approximation for large dataset.
  • Now using BiocSingular to manage all SVD components.
  • Now automatically remove zeroes in the rows and columns of the SCE.

scMerge 1.1.5

  • Adding version restrictions on S4Vectors and SingleCellExperiment dependent packages.

scMerge 1.1.4

  • plot_igraph would allow suppression of igraph output during unsupervised scMerge

scMerge 1.1.3

  • Column name must be non-NULL and without duplicates

scMerge 1.1.2

  • Resolved problems with only a single linking cell-type across multiple batches

scMerge 1.1.0

  • Accepted by Bioconductor

scMerge 0.99 (development version)

scMerge 0.99.24

  • Updated ciation information due to PNAS acceptance.

scMerge 0.99.23

  • Fixed assignment based on feedbacks

scMerge 0.99.21

  • Increase code coverage to 85%.

scMerge 0.99.20

  • Updated vignette on SEGs and manuals

scMerge 0.99.19

  • Fixed spelling
  • Added verbose option
  • Code coverage at 75 percent (more tests on error handling needed)

scMerge 0.99.17

  • Fixed README install_github vignette issue.
  • Fixed pkgdown organisation issue.
  • Major updates on the scReplicate function: more informative messages.
  • Using cross-product of matrix to perform SVD to speed up calculations.
  • Added testing scripts.
  • Fixed vignette text output issues.

scMerge 0.99.11

  • Reduced data size in scMerge to pass BioC checks