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 0.0.0.9003
Added the option to downsample faceted plots to the bb_var_umap function.
blaseRtools 0.0.0.9004
Fixed go term functions.
blaseRtools 0.0.0.9005
Made it possible to explicitly order axes in bb_gene_dotplot
blaseRtools 0.0.0.9006-7
Edits to violin plot to allow automatic matching of point to violin.
blaseRtools 0.0.0.9008
reworked print stats report
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 0.0.0.9018
added cell and feature metadata functions.
blaseRtools 0.0.0.9019-20
added blind and unblind functions
blaseRtools 0.0.0.9021-25
edited blind function and tbl_to_coldata and tbl_to_rowdata functions
blaseRtools 0.0.0.9026
add bb_plotfootprint function from signac
blaseRtools 0.0.0.9027-32
added ape class and functions
blaseRtools 0.0.0.9033
fixed glitch in tbl to coldata and tbl to rowdata
blaseRtools 0.0.0.9034-6
added hg38_ape
blaseRtools 0.0.0.9037
fixed plyranges namespace issue
blaseRtools 0.0.0.9038
fixed Ape.fimo color bug
blaseRtools 0.0.0.9039
Added trace class and functions
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 0.0.0.9042
externalized data objects for certain functions
blaseRtools 0.0.0.9045
added metafeature functions
blaseRtools 0.0.0.9046
added bb_load_tenx_targz and removed other 10X loading functions since they were very confusing.
blaseRtools 0.0.0.9047
added bb_cluster_representation
blaseRtools 0.0.0.9048
added bb_pseudobulk_mf
blaseRtools 0.0.0.9049
added scRNA-seq vignette
blaseRtools 0.0.0.9050
added bb_extract_msig
blaseRtools 0.0.0.9051
fixed pseudobulk mf
blaseRtools 0.0.0.9052
Ape vignette, fixed bugs in Ape functions and bb_renv_datapkg.
blaseRtools 0.0.0.9053-4
Changes to bb_gene_dotplot
blaseRtools 0.0.0.9055
Changed dependencies
blaseRtools 0.0.0.9056
Added filter_cds
blaseRtools 0.0.0.9057
edited dependencies
blaseRtools 0.0.0.9058
added bb_cds_anno and bb_cds_heatmap functions
blaseRtools 0.0.0.9059 - 61
edited DESCRIPTION to include ComplexHeatmap
blaseRtools 0.0.0.9064
edited dependencies to include tidyverse as depends
blaseRtools 0.0.0.9065
added citeseq functions
blaseRtools 0.0.0.9066
increased default brightness of bb_gene_umap color scale
blaseRtools 0.0.0.9067
fixed bug in citeseq functions where object got converted to wrong class
blaseRtools 0.0.0.9068
fixed spot in pseudobulk where it converted sparse to dense unnecessarily
blaseRtools 0.0.0.9069
added cellchat functions
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 0.0.0.9080
edited dependencies
blaseRtools 0.0.0.9090 - 94
ported many essential functions to take in Seurat and cds objects.
blaseRtools 0.0.0.9095
added max expression value parameter to bb_gene_umap
blaseRtools 0.0.0.9096
added geom split violin
blaseRtools 0.0.0.9097
reversed order of link plotting in trace_funcs.R
now highest scoring link is plotted on top
blaseRtools 0.0.0.9098-100
added rasterize option to umap and violin plot functions
blaseRtools 0.0.0.9101
added alt dims to bb_gene_umap
blaseRtools 0.0.0.9102
added font face option to plot trace model function
blaseRtools 0.0.0.9103
added split atac function
new parameter in bb_qc to set alternate cutoffs
blaseRtools 0.0.0.9104
edited split citeseq withDimnames param
blaseRtools 0.0.0.9105
added label option to bb_var_umap
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 0.0.0.9109
added expression_threshold to genebubbles
blaseRtools 0.0.0.9110
debugged cite umap
blaseRtools 0.0.0.9111
debugged gene umap plotting aggregate genes
blaseRtools 0.0.0.9112-3
debugged bb_rowmeta and bb_aggregate experiment names parameter
blaseRtools 0.0.0.9114
added normalize_batch()
blaseRtools 0.0.0.9115
edited bb_citeseq to optionally order cells to plot
blaseRtools 0.0.0.9116
removed matrix.utils dependency
blaseRtools 0.0.0.9117-24
removed seurat wrappers dependency
removed renv dependency
edited git ignore
added vignettes to buildignore
removed examples
blaseRtools 0.0.0.9117-25
added assay option to cite umap
blaseRtools 0.0.0.9126 - 30
major update to ape functions
refactored
corrected bugs
added transcriptome APE function
blaseRtools 0.0.0.9132
added bb_cluster_representation2
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 0.0.0.9135-6
debugged seurat_anno
blaseRtools 0.0.0.9137-8
pseuodime functions
blaseRtools 0.0.0.9139
added plot geens in pseudotime
blaseRtools 0.0.0.9140-1
fixed transcriptome ape function
blaseRtools 0.0.0.9142
added outline function to bb_var_umap
blaseRtools 0.0.0.9143
fixed bug where factors got lost from bb_genebubbles
blaseRtools 0.0.0.9144
updated blind and unblind functions to use fs::path
added blinding vignette
blaseRtools 0.0.0.9145-6
major updates to trace functions
blaseRtools 0.0.0.9147
updated ape function to put placeholder feature in gbk files without features.
blaseRtools 0.0.0.9148
updated bb_doubletfinder to work with seurat v5
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 0.0.0.9154 -55
added bb_fragment_replacement
blaseRtools 0.0.0.9156
edited get_seurat_clr to fix bug introduced by Seurat v5
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
blaseRtools 0.0.0.9161
fixed a bug where filter_cds returned all cells instead of 0 cells
blaseRtools 0.0.0.9162
parameterized bb_qc to change nmads
blaseRtools 0.0.0.9163
added minimum segment length parameter to bb_var_umap