NEWS.md

In jackbibby1/SCPA: Single Cell Pathway Analysis

SCPA v1.6.2

Default to cores = 3 if parallel = TRUE is supplied with no cores argument

SCPA v1.6.1

Minor changes

Add compatability for numeric vectors in compare_seurat()

SCPA v1.6

Major changes

Updated compatability with Seurat v5. compare_seurat() and seurat_extract() automatically detect Seurat object version

SCPA v1.5.4

Minor changes

Change package dependeny version to improve installation

SCPA v1.5.2

Minor changes

Ability to specify multiple gmt filepaths in the pathway argument of compare_pathways(). For examples see here

SCPA v1.5.1

Minor changes

Fix downsample so it isn't forcing 500 cells #34

SCPA v1.5.0

Major changes

• Parallel processing is now built into into the compare_pathways(), compare_seurat(), and compare_sce() functions. Users just need to specify parallel = TRUE and cores = x to use parallel processing instead of calling compare_pathways_parallel()

Minor changes

• Fix downsample #31

SCPA v1.4.0

Major changes

• Parallel implementation for compare_pathways() via compare_pathways_parallel(). Users can specify number of cores to run in the pathway comparison

SCPA v1.3.0

Major changes

• The main function of SCPA has been rewritten to be much more efficient with memory usage. This means that RAM availability is likely not going to be limiting on a typical computer i.e. 8GB RAM, even with a huge number of comparisons.
• The speed of the pathway comparisons is also slightly improved

Minor changes

• Added the option to filter gene set size in compare_seurat()

SCPA v1.2.1

Minor changes

• Add functionality to choose assay in Seurat object

SCPA v1.2

Major changes

• Add functionality to deal with SingleCellExperiment objects
• sce_extract can now extract data from SCE objects based on colData
• compare_sce can now compare pathways directly within an SCE object

SCPA v1.1

Major changes

• Add functionality to visualise results from SCPA with plot_rank() and plot_heatmap()

Minor changes

• Improve messaging with compare_pathways()

SCPA v1.0.0

Minor changes

• Allow usage of multiple file types for pathways e.g. gmt, csv
• Fix CRAN archive with multicross and crossmatch

SCPA v0.0.0.9000

• Release SCPA for multivariate testing of pathways in scRNA-seq data

jackbibby1/SCPA documentation built on May 14, 2024, 7:16 a.m.