Changelog
Source:NEWS.md
blaseRtools 0.0.0.9000
- Made a new gene dotplot function to allow multifactorial plotting. Added a function to color cells by local number in bb_var_umap.
blaseRtools 0.0.0.9001
- Made a new function, bb_align, calculates aligned umap coordinates. These are inserted into the internal dimension slot of the CDS object. Prealignment coordinates are added as new cell metadata columns.
blaseRtools 0.0.0.9002
- Fixed a bug in bb_var_umap for local_n and log_local_n plotting when faceting by 1 dimension.
blaseRtools 0.0.0.9009-10
- changed bb_load_multi_counts to be compatible with cellranger v6, changed qc to allow for pdx
blaseRtools 0.0.0.9011
- added bb_renv_datapkg: a function to load binary data packages from local sources
blaseRtools 0.0.0.9012
- added bb_goenrichment back to namespace; edited bb_renv_datapkg to allow installation of explicit binary packages
blaseRtools 0.0.0.9013 - 15
- updated bb_renv_datapkg to check for and install latest package version.
blaseRtools 0.0.0.9016-17
- new function bb_load_cloud_counts for compatibility with 10X cloud preprocessing output.
blaseRtools 0.0.0.9040
- Removed dependency on plyranges since it was causing so many conflicts and was difficult to install.
- Changed for importing functions from DESeq2 and DoubletFinder
blaseRtools 0.0.0.9041
- Fixed load cloud counts not to err on multi-genome samples. Now it will load all genomes and then you have to remove the ones you don’t want from the cds. Just easier to do it that way.
blaseRtools 0.0.0.9046
- added bb_load_tenx_targz and removed other 10X loading functions since they were very confusing.
blaseRtools 0.0.0.9075-9
- edited pseudobulk mf to choose vst with large number of samples
- added back cellchat
- silenced warnings on bb_gene_umap and bb_var_umap
blaseRtools 0.0.0.9097
- reversed order of link plotting in trace_funcs.R
- now highest scoring link is plotted on top
blaseRtools 0.0.0.9106
- added option to show alt experiment in bb_rowmeta
- debugged bb_cite_umap
- changed x, y labels in bb_gene_umap
blaseRtools 0.0.0.9107-108
- added option to plot antibody capture in gene bubbles
- made changes in bb_aggregate to support this
blaseRtools 0.0.0.9117-24
- removed seurat wrappers dependency
- removed renv dependency
- edited git ignore
- added vignettes to buildignore
- removed examples
blaseRtools 0.0.0.9126 - 30
- major update to ape functions
- refactored
- corrected bugs
- added transcriptome APE function
blaseRtools 0.0.0.9133-4
- added bb_load_tensx_h5
- edited bb_split_citeseq to recalculate size factors after removing the antibody matrix
blaseRtools 0.0.0.9147
- updated ape function to put placeholder feature in gbk files without features.
blaseRtools 0.0.0.9149-51
- fixed bugs in trace functions related to trimming levels for the peaks slot.
- added option to debug the gene model track by showing the plotted transcript IDs
blaseRtools 0.0.0.9152-3
- fixed bug where density var umap plots with two dimensions weren’t being calculated correctly.
blaseRtools 0.0.0.9157
- fixed bug in bb_cds_anno where joining the new cell annotations back onto the cds cell metadata failed due to failure to specify the joining columns. This was only evident with cds queries containing conflicting cell metadata columns like RNA counts etc and resulted in NA assignments.
blaseRtools 0.0.0.9158-9
- fixed bug in bb_cite_umap where we were matching additional antibodies inappropriately
blaseRtools 0.0.0.9160:
- handled case when certain single cell objects do not have a gene_short_name column
- applies to gene_umap and genebubbles
- internal function get_gene_ids