NEWS.md

In SydneyBioX/scMerge: scMerge: Merging multiple batches of scRNA-seq data

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

SydneyBioX/scMerge documentation built on April 14, 2024, 3:22 a.m.