NEWS

---

blaseRtools 0.0.0.9163

• added minimum segment length parameter to bb_var_umap

blaseRtools 0.0.0.9162

• parameterized bb_qc to change nmads

blaseRtools 0.0.0.9161

• fixed a bug where filter_cds returned all cells instead of 0 cells

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 0.0.0.9158-9

• fixed bug in bb_cite_umap where we were matching additional antibodies inappropriately

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 0.0.0.9156

• edited get_seurat_clr to fix bug introduced by Seurat v5

blaseRtools 0.0.0.9154

• added bb_fragment_replacement

blaseRtools 0.0.0.9152-3

• fixed bug where density var umap plots with two dimensions weren't being calculated correctly.

blaseRtools 0.0.0.9149-51

• 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 0.0.0.9148

• updated bb_doubletfinder to work with seurat v5

blaseRtools 0.0.0.9147

• updated ape function to put placeholder feature in gbk files without features.

blaseRtools 0.0.0.9145-6

• major updates to trace functions

blaseRtools 0.0.0.9144

• updated blind and unblind functions to use fs::path
• added blinding vignette

blaseRtools 0.0.0.9143

• fixed bug where factors got lost from bb_genebubbles

blaseRtools 0.0.0.9142

• added outline function to bb_var_umap

blaseRtools 0.0.0.9140-1

• fixed transcriptome ape function

blaseRtools 0.0.0.9139

• added plot geens in pseudotime

blaseRtools 0.0.0.9137-8

• pseuodime functions

blaseRtools 0.0.0.9135-6

• debugged seurat_anno

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 0.0.0.9132

• added bb_cluster_representation2

blaseRtools 0.0.0.9126

• major update to ape functions
• refactored
• corrected bugs
• added transcriptome APE function

blaseRtools 0.0.0.9117-25

• added assay option to cite umap

blaseRtools 0.0.0.9117-24

• removed seurat wrappers dependency
• removed renv dependency
• edited git ignore
• added vignettes to buildignore
• removed examples

blaseRtools 0.0.0.9116

• removed matrix.utils dependency

blaseRtools 0.0.0.9115

• edited bb_citeseq to optionally order cells to plot

blaseRtools 0.0.0.9114

• added normalize_batch()

blaseRtools 0.0.0.9112-3

• debugged bb_rowmeta and bb_aggregate experiment names parameter

blaseRtools 0.0.0.9111

• debugged gene umap plotting aggregate genes

blaseRtools 0.0.0.9110

• debugged cite umap

blaseRtools 0.0.0.9109

• added expression_threshold to genebubbles

blaseRtools 0.0.0.9107-108

• added option to plot antibody capture in gene bubbles
• made changes in bb_aggregate to support this

blaseRtools 0.0.0.9106

• added option to show alt experiment in bb_rowmeta
• debugged bb_cite_umap
• changed x, y labels in bb_gene_umap

blaseRtools 0.0.0.9105

• added label option to bb_var_umap

blaseRtools 0.0.0.9104

• edited split citeseq withDimnames param

blaseRtools 0.0.0.9103

• added split atac function
• new parameter in bb_qc to set alternate cutoffs

blaseRtools 0.0.0.9102

• added font face option to plot trace model function

blaseRtools 0.0.0.9101

• added alt dims to bb_gene_umap

blaseRtools 0.0.0.9098-100

• added rasterize option to umap and violin plot functions

blaseRtools 0.0.0.9097

• reversed order of link plotting in trace_funcs.R
• now highest scoring link is plotted on top

blaseRtools 0.0.0.9096

• added geom split violin

blaseRtools 0.0.0.9095

• added max expression value parameter to bb_gene_umap

blaseRtools 0.0.0.9090

• ported many essential functions to take in Seurat and cds objects.

blaseRtools 0.0.0.9080

• edited dependencies

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 0.0.0.9069

• added cellchat functions

blaseRtools 0.0.0.9068

• fixed spot in pseudobulk where it converted sparse to dense unnecessarily

blaseRtools 0.0.0.9067

• fixed bug in citeseq functions where object got converted to wrong class

blaseRtools 0.0.0.9066

• increased default brightness of bb_gene_umap color scale

blaseRtools 0.0.0.9065

• added citeseq functions

blaseRtools 0.0.0.9064

• edited dependencies to include tidyverse as depends

blaseRtools 0.0.0.9059

• edited DESCRIPTION to include ComplexHeatmap

blaseRtools 0.0.0.9058

• added bb_cds_anno and bb_cds_heatmap functions

blaseRtools 0.0.0.9057

• edited dependencies

blaseRtools 0.0.0.9056

• Added filter_cds

blaseRtools 0.0.0.9055

• Changed dependencies

blaseRtools 0.0.0.9053-4

• Changes to bb_gene_dotplot

blaseRtools 0.0.0.9052

• Ape vignette, fixed bugs in Ape functions and bb_renv_datapkg.

blaseRtools 0.0.0.9051

• fixed pseudobulk mf

blaseRtools 0.0.0.9050

• added bb_extract_msig

blaseRtools 0.0.0.9049

• added scRNA-seq vignette

blaseRtools 0.0.0.9048

• added bb_pseudobulk_mf

blaseRtools 0.0.0.9047

• added bb_cluster_representation

blaseRtools 0.0.0.9046

• added bb_load_tenx_targz and removed other 10X loading functions since they were very confusing.

blaseRtools 0.0.0.9045

• added metafeature functions

blaseRtools 0.0.0.9042

• externalized data objects for certain functions

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 0.0.0.9040

• 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 0.0.0.9039

• Added trace class and functions

blaseRtools 0.0.0.9038

• fixed Ape.fimo color bug

blaseRtools 0.0.0.9037

• fixed plyranges namespace issue

blaseRtools 0.0.0.9034-6

• added hg38_ape

blaseRtools 0.0.0.9033

• fixed glitch in tbl to coldata and tbl to rowdata

blaseRtools 0.0.0.9027-32

• added ape class and functions

blaseRtools 0.0.0.9026

• add bb_plotfootprint function from signac

blaseRtools 0.0.0.9021-25

• edited blind function and tbl_to_coldata and tbl_to_rowdata functions

blaseRtools 0.0.0.9019-20

• added blind and unblind functions

blaseRtools 0.0.0.9018

• added cell and feature metadata functions.

blaseRtools 0.0.0.9016-17

• new function bb_load_cloud_counts for compatibility with 10X cloud preprocessing output.

blaseRtools 0.0.0.9013

• updated bb_renv_datapkg to check for and install latest package version.

blaseRtools 0.0.0.9012

• added bb_goenrichment back to namespace; edited bb_renv_datapkg to allow installation of explicit binary packages

blaseRtools 0.0.0.9011

• added bb_renv_datapkg: a function to load binary data packages from local sources

blaseRtools 0.0.0.9009-10

• changed bb_load_multi_counts to be compatible with cellranger v6, changed qc to allow for pdx

blaseRtools 0.0.0.9008

• reworked print stats report

blaseRtools 0.0.0.9006-7

• Edits to violin plot to allow automatic matching of point to violin.

blaseRtools 0.0.0.9005

• Made it possible to explicitly order axes in bb_gene_dotplot

blaseRtools 0.0.0.9004

• Fixed go term functions.

blaseRtools 0.0.0.9003

• Added the option to downsample faceted plots to the bb_var_umap function.

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 0.0.0.9001

• 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 0.0.0.9000

• Made a new gene dotplot function to allow multifactorial plotting. Added a function to color cells by local number in bb_var_umap.