Changes in version 0.0.0.9208 - added bb_souporcell_matrix Changes in version 0.0.0.9207 - debugged bb_cite_umap - debugged SummarizedHeatmap - Added option to split citeseq in bb_load_tenx_h5 - removed bb_load_tenx_targz Changes in version 0.0.0.9206 - added geom-sig-table Changes in version 0.0.0.9205 - updated blind images to correct edge cases Changes in version 0.0.0.9203-4 - modified bb_make_trace to facilitate visualization of small ranges without centering on a gene. - modified bb_plot_gene_model to avoid dropping tiles - modified bb_plot_gene_model to extend arrow segments to the end of the gene Changes in version 0.0.0.9198-2002 - removed grr dependency from Matrix.utils, potentially affecting bb_gene_umap and bb_pseudobulk_mf. Testing seems ok. - moved in project_data from blaseRtemplates Changes in version 0.0.0.9196-7 - removed dependency on plyranges::filter which was removed upstream - used ChatGPT to clean up trace_funcs.R; prelim testing seems ok. Changes in version 0.0.0.9191-5 - fixed bug in filter_cds that returned all of the cells if filtering returns 0 lines - fixed namespace issues in bb_doubletfinder Changes in version 0.0.0.9189 - fixed bb_blind_images Changes in version 0.0.0.9188 - added bb_import_macs_narrowpeak Changes in version 0.0.0.9184 - summarized heatmap Changes in version 0.0.0.9183 - Updated trace functions to fill in gaps in sparse traces Changes in version 0.0.0.9182 - SummarizedHeatmap Changes in version 0.0.0.9177-81 - pseudocells - monocle projection Changes in version 0.0.0.9174-6 - renamed as_tibble to ImageCatalog.as_tibble - fixed scRNA-seq vignette Changes in version 0.0.0.9173 - added ImageClass Changes in version 0.0.0.9171 - fixes bug in cellchat to work with on disk matrices Changes in version 0.0.0.9170 - imports newest monocle3 Changes in version 0.0.0.9169 - added monocle anno Changes in version 0.0.0.9168 - fixed bug in bb_seurat_anno where cds was misidentified Changes in version 0.0.0.9167 - fixed bug Changes in version 0.0.0.9166 - added hexify to bb_var_umap - changed the interaction label used by bb_cellchat_heatmap because of duplications in the cellchat database. This may cause cosmetic changes in old code. Changes in version 0.0.0.9165 - added bb_daseq Changes in version 0.0.0.9164 - added bb_loupeR function Changes in version 0.0.0.9163 - added minimum segment length parameter to bb_var_umap Changes in version 0.0.0.9162 - parameterized bb_qc to change nmads Changes in version 0.0.0.9161 - fixed a bug where filter_cds returned all cells instead of 0 cells Changes in version 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 Changes in version 0.0.0.9158-9 - fixed bug in bb_cite_umap where we were matching additional antibodies inappropriately Changes in version 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. Changes in version 0.0.0.9156 - edited get_seurat_clr to fix bug introduced by Seurat v5 Changes in version 0.0.0.9154 - added bb_fragment_replacement Changes in version 0.0.0.9152-3 - fixed bug where density var umap plots with two dimensions weren't being calculated correctly. Changes in version 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 Changes in version 0.0.0.9148 - updated bb_doubletfinder to work with seurat v5 Changes in version 0.0.0.9147 - updated ape function to put placeholder feature in gbk files without features. Changes in version 0.0.0.9145-6 - major updates to trace functions Changes in version 0.0.0.9144 - updated blind and unblind functions to use fs::path - added blinding vignette Changes in version 0.0.0.9143 - fixed bug where factors got lost from bb_genebubbles Changes in version 0.0.0.9142 - added outline function to bb_var_umap Changes in version 0.0.0.9140-1 - fixed transcriptome ape function Changes in version 0.0.0.9139 - added plot geens in pseudotime Changes in version 0.0.0.9137-8 - pseuodime functions Changes in version 0.0.0.9135-6 - debugged seurat_anno Changes in version 0.0.0.9133-4 - added bb_load_tensx_h5 - edited bb_split_citeseq to recalculate size factors after removing the antibody matrix Changes in version 0.0.0.9132 - added bb_cluster_representation2 Changes in version 0.0.0.9126 - major update to ape functions - refactored - corrected bugs - added transcriptome APE function Changes in version 0.0.0.9117-25 - added assay option to cite umap Changes in version 0.0.0.9117-24 - removed seurat wrappers dependency - removed renv dependency - edited git ignore - added vignettes to buildignore - removed examples Changes in version 0.0.0.9116 - removed matrix.utils dependency Changes in version 0.0.0.9115 - edited bb_citeseq to optionally order cells to plot Changes in version 0.0.0.9114 - added normalize_batch() Changes in version 0.0.0.9112-3 - debugged bb_rowmeta and bb_aggregate experiment names parameter Changes in version 0.0.0.9111 - debugged gene umap plotting aggregate genes Changes in version 0.0.0.9110 - debugged cite umap Changes in version 0.0.0.9109 - added expression_threshold to genebubbles Changes in version 0.0.0.9107-108 - added option to plot antibody capture in gene bubbles - made changes in bb_aggregate to support this Changes in version 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 Changes in version 0.0.0.9105 - added label option to bb_var_umap Changes in version 0.0.0.9104 - edited split citeseq withDimnames param Changes in version 0.0.0.9103 - added split atac function - new parameter in bb_qc to set alternate cutoffs Changes in version 0.0.0.9102 - added font face option to plot trace model function Changes in version 0.0.0.9101 - added alt dims to bb_gene_umap Changes in version 0.0.0.9098-100 - added rasterize option to umap and violin plot functions Changes in version 0.0.0.9097 - reversed order of link plotting in trace_funcs.R - now highest scoring link is plotted on top Changes in version 0.0.0.9096 - added geom split violin Changes in version 0.0.0.9095 - added max expression value parameter to bb_gene_umap Changes in version 0.0.0.9090 - ported many essential functions to take in Seurat and cds objects. Changes in version 0.0.0.9080 - edited dependencies Changes in version 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 Changes in version 0.0.0.9069 - added cellchat functions Changes in version 0.0.0.9068 - fixed spot in pseudobulk where it converted sparse to dense unnecessarily Changes in version 0.0.0.9067 - fixed bug in citeseq functions where object got converted to wrong class Changes in version 0.0.0.9066 - increased default brightness of bb_gene_umap color scale Changes in version 0.0.0.9065 - added citeseq functions Changes in version 0.0.0.9064 - edited dependencies to include tidyverse as depends Changes in version 0.0.0.9059 - edited DESCRIPTION to include ComplexHeatmap Changes in version 0.0.0.9058 - added bb_cds_anno and bb_cds_heatmap functions Changes in version 0.0.0.9057 - edited dependencies Changes in version 0.0.0.9056 - Added filter_cds Changes in version 0.0.0.9055 - Changed dependencies Changes in version 0.0.0.9053-4 - Changes to bb_gene_dotplot Changes in version 0.0.0.9052 - Ape vignette, fixed bugs in Ape functions and bb_renv_datapkg. Changes in version 0.0.0.9051 - fixed pseudobulk mf Changes in version 0.0.0.9050 - added bb_extract_msig Changes in version 0.0.0.9049 - added scRNA-seq vignette Changes in version 0.0.0.9048 - added bb_pseudobulk_mf Changes in version 0.0.0.9047 - added bb_cluster_representation Changes in version 0.0.0.9046 - added bb_load_tenx_targz and removed other 10X loading functions since they were very confusing. Changes in version 0.0.0.9045 - added metafeature functions Changes in version 0.0.0.9042 - externalized data objects for certain functions Changes in version 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. Changes in version 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 Changes in version 0.0.0.9039 - Added trace class and functions Changes in version 0.0.0.9038 - fixed Ape.fimo color bug Changes in version 0.0.0.9037 - fixed plyranges namespace issue Changes in version 0.0.0.9034-6 - added hg38_ape Changes in version 0.0.0.9033 - fixed glitch in tbl to coldata and tbl to rowdata Changes in version 0.0.0.9027-32 - added ape class and functions Changes in version 0.0.0.9026 - add bb_plotfootprint function from signac Changes in version 0.0.0.9021-25 - edited blind function and tbl_to_coldata and tbl_to_rowdata functions Changes in version 0.0.0.9019-20 - added blind and unblind functions Changes in version 0.0.0.9018 - added cell and feature metadata functions. Changes in version 0.0.0.9016-17 - new function bb_load_cloud_counts for compatibility with 10X cloud preprocessing output. Changes in version 0.0.0.9013 - updated bb_renv_datapkg to check for and install latest package version. Changes in version 0.0.0.9012 - added bb_goenrichment back to namespace; edited bb_renv_datapkg to allow installation of explicit binary packages Changes in version 0.0.0.9011 - added bb_renv_datapkg: a function to load binary data packages from local sources Changes in version 0.0.0.9009-10 - changed bb_load_multi_counts to be compatible with cellranger v6, changed qc to allow for pdx Changes in version 0.0.0.9008 - reworked print stats report Changes in version 0.0.0.9006-7 - Edits to violin plot to allow automatic matching of point to violin. Changes in version 0.0.0.9005 - Made it possible to explicitly order axes in bb_gene_dotplot Changes in version 0.0.0.9004 - Fixed go term functions. Changes in version 0.0.0.9003 - Added the option to downsample faceted plots to the bb_var_umap function. Changes in version 0.0.0.9002 - Fixed a bug in bb_var_umap for local_n and log_local_n plotting when faceting by 1 dimension. Changes in version 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. Changes in version 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.