Files in blaserlab/blaseRtools
R Tools for Blaser Lab Data Analysis
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/Image.R
R/Matrix.utils.R
R/SummarizedHeatmap.R
R/ape_class.R
R/ape_helpers.R
R/ape_make.R
R/atac.R
R/bb_align.R
R/bb_annotate_npc.R
R/bb_blind_images.R
R/bb_cds_anno.R
R/bb_cds_heatmap.R
R/bb_cluster_representation.R
R/bb_cluster_representation2.R
R/bb_da_seq.R
R/bb_datahelpers.R
R/bb_doubletfinder.R
R/bb_extract_msig.R
R/bb_fix_file_path.R
R/bb_fragments.R
R/bb_gene_dotplot.R
R/bb_gene_modules.R
R/bb_gene_pseudotime.R
R/bb_gene_umap.R
R/bb_gene_violinplot.R
R/bb_genebubbles.R
R/bb_goenrichment.R
R/bb_goscatter.R
R/bb_gosummary.R
R/bb_load_tenx.R
R/bb_loupeR.R
R/bb_meta.R
R/bb_monocle_anno_project.R
R/bb_monocle_regression.R
R/bb_operators.R
R/bb_parseape.R
R/bb_plot_rowData_col.R
R/bb_plotfootprint.R
R/bb_print_full_stats.R
R/bb_pseudobulk_mf.R
R/bb_pseudotime.R
R/bb_qc.R
R/bb_rejoin.R
R/bb_remove_dupes.R
R/bb_seurat_anno.R
R/bb_tbl_to_coldata.R
R/bb_tbl_to_matrix.R
R/bb_tbl_to_rowdata.R
R/bb_triplecluster.R
R/bb_unblind.R
R/bb_var_umap.R
R/cellchat.R
R/cistopic_go.R
R/citeseq.R
R/filter_cds.R
R/geoms.R
R/heatmap_plotting.R
R/heatmap_themes.R
R/metafeature_funcs.R
R/normalize_batch.R
R/pseudocells.R
R/sw_internal.R
R/sw_monocle3.R
R/trace_funcs.R
README.md
_pkgdown.yml
blaseRtools.Rproj
data-raw/projection.R
data-raw/scratch.R
data-raw/scratch_load_process.R
data-raw/testing.R
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/articles/Ape.html
docs/articles/SummarizedHeatmap.html
docs/articles/SummarizedHeatmap_files/figure-html/unnamed-chunk-10-1.png
docs/articles/SummarizedHeatmap_files/figure-html/unnamed-chunk-11-1.png
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docs/articles/SummarizedHeatmap_files/figure-html/unnamed-chunk-9-2.png
docs/articles/blind_images.html
docs/articles/index.html
docs/articles/scRNAseq.html
docs/articles/scRNAseq_files/figure-html/unnamed-chunk-16-1.png
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docs/articles/trace.html
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docs/authors.html
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docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map
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docs/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js
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docs/deps/data-deps.txt
docs/deps/font-awesome-6.4.2/css/all.css
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docs/deps/headroom-0.11.0/jQuery.headroom.min.js
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docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
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docs/index.html
docs/katex-auto.js
docs/lightswitch.js
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docs/pages/Ape.R
docs/pages/Ape.html
docs/pages/scRNAseq.R
docs/pages/scRNAseq.html
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Ape-class.html
docs/reference/Ape.DNA.html
docs/reference/Ape.fasta.html
docs/reference/Ape.fimo.html
docs/reference/Ape.granges.html
docs/reference/Ape.save.html
docs/reference/Ape.setFeatures.html
docs/reference/COMMENTS.html
docs/reference/FEATURES.html
docs/reference/Image-class.html
docs/reference/ImageCatalog-class.html
docs/reference/LOCUS.html
docs/reference/LearnGraph.html
docs/reference/Rplot001.png
docs/reference/SeuratWrappers-package.html
docs/reference/SummarizedHeatmap.html
docs/reference/Trace-class.html
docs/reference/Trace.data.html
docs/reference/Trace.features.html
docs/reference/Trace.gene_model.html
docs/reference/Trace.links.html
docs/reference/Trace.peaks.html
docs/reference/Trace.plot_range.html
docs/reference/Trace.setData.html
docs/reference/Trace.setFeatures.html
docs/reference/Trace.setLinks.html
docs/reference/Trace.setRange.html
docs/reference/Trace.setpeaks.html
docs/reference/add_cds_factor_columns.html
docs/reference/aggregate.Matrix.html
docs/reference/as.Seurat.extras.html
docs/reference/as.cell_data_set.html
docs/reference/bb_aggregate.html
docs/reference/bb_align.html
docs/reference/bb_annotate_npc.html
docs/reference/bb_blind_images.html
docs/reference/bb_buff_granges.html
docs/reference/bb_cds_anno.html
docs/reference/bb_cds_heatmap.html
docs/reference/bb_cellchat.html
docs/reference/bb_cellchat_heatmap.html
docs/reference/bb_cellmeta.html
docs/reference/bb_cite_umap.html
docs/reference/bb_cluster_representation.html
docs/reference/bb_cluster_representation2.html
docs/reference/bb_daseq.html
docs/reference/bb_doubletfinder.html
docs/reference/bb_extract_msig.html
docs/reference/bb_fix_file_path.html
docs/reference/bb_fragment_replacement.html
docs/reference/bb_gene_dotplot.html
docs/reference/bb_gene_modules.html
docs/reference/bb_gene_pseudotime.html
docs/reference/bb_gene_umap.html
docs/reference/bb_gene_violinplot.html
docs/reference/bb_genebubbles.html
docs/reference/bb_goenrichment.html
docs/reference/bb_goscatter.html
docs/reference/bb_gosummary.html
docs/reference/bb_import_bw.html
docs/reference/bb_import_seacr_peaks.html
docs/reference/bb_load_tenx_h5.html
docs/reference/bb_load_tenx_targz.html
docs/reference/bb_loupeR.html
docs/reference/bb_makeTrace.html
docs/reference/bb_make_ape_genomic.html
docs/reference/bb_make_ape_transcript.html
docs/reference/bb_merge_narrowpeaks.html
docs/reference/bb_metafeature.html
docs/reference/bb_monocle_.html
docs/reference/bb_monocle_anno.html
docs/reference/bb_monocle_regression.html
docs/reference/bb_monocle_regression_better.html
docs/reference/bb_parseape.html
docs/reference/bb_plot_genes_in_pseudotime.html
docs/reference/bb_plot_heatmap_colData.html
docs/reference/bb_plot_heatmap_colDendro.html
docs/reference/bb_plot_heatmap_colHighlight.html
docs/reference/bb_plot_heatmap_main.html
docs/reference/bb_plot_heatmap_rowData.html
docs/reference/bb_plot_heatmap_rowDendro.html
docs/reference/bb_plot_heatmap_rowHighlight.html
docs/reference/bb_plot_rowData_col.html
docs/reference/bb_plot_trace_axis.html
docs/reference/bb_plot_trace_data.html
docs/reference/bb_plot_trace_feature.html
docs/reference/bb_plot_trace_links.html
docs/reference/bb_plot_trace_model.html
docs/reference/bb_plot_trace_peaks.html
docs/reference/bb_plotfootprint.html
docs/reference/bb_print_full_stats.html
docs/reference/bb_promoter_overlap.html
docs/reference/bb_pseudobulk_mf.html
docs/reference/bb_pseudocells.html
docs/reference/bb_pseudotime.html
docs/reference/bb_qc.html
docs/reference/bb_read_bam.html
docs/reference/bb_read_narrowpeak.html
docs/reference/bb_rejoin.html
docs/reference/bb_remove_dupes.html
docs/reference/bb_rowmeta.html
docs/reference/bb_seurat_anno.html
docs/reference/bb_singlecell_anno.html
docs/reference/bb_split_atac.html
docs/reference/bb_split_citeseq.html
docs/reference/bb_tbl_to_coldata.html
docs/reference/bb_tbl_to_matrix.html
docs/reference/bb_tbl_to_rowdata.html
docs/reference/bb_triplecluster.html
docs/reference/bb_unblind_images.html
docs/reference/bb_var_umap.html
docs/reference/dMcast.html
docs/reference/data_median_se.html
docs/reference/data_summary_mean_sd.html
docs/reference/data_summary_mean_se.html
docs/reference/data_summary_median_iqr.html
docs/reference/data_summary_median_mad.html
docs/reference/filter_cds.html
docs/reference/geom_split_violin.html
docs/reference/granges_to_features.html
docs/reference/grapes-notin-grapes.html
docs/reference/index.html
docs/reference/merge.Matrix.html
docs/reference/normalize_batch.html
docs/reference/rBind.fill.html
docs/reference/se.html
docs/reference/show-Ape-method.html
docs/reference/show-Trace-method.html
docs/search.json
docs/sitemap.xml
library_catalogs/blas02_blaseRtools.tsv
man/Ape-class.Rd
man/Ape.DNA.Rd
man/Ape.fasta.Rd
man/Ape.fimo.Rd
man/Ape.granges.Rd
man/Ape.save.Rd
man/Ape.setFeatures.Rd
man/COMMENTS.Rd
man/FEATURES.Rd
man/Image-class.Rd
man/ImageCatalog-class.Rd
man/LOCUS.Rd
man/LearnGraph.Rd
man/SeuratWrappers-package.Rd
man/SummarizedHeatmap.Rd
man/Trace-class.Rd
man/Trace.data.Rd
man/Trace.gene_model.Rd
man/Trace.links.Rd
man/Trace.peaks.Rd
man/Trace.plot_range.Rd
man/Trace.setData.Rd
man/Trace.setLinks.Rd
man/Trace.setRange.Rd
man/Trace.setpeaks.Rd
man/add_cds_factor_columns.Rd
man/aggregate.Matrix.Rd
man/as.Seurat.extras.Rd
man/as.cell_data_set.Rd
man/bb_aggregate.Rd
man/bb_align.Rd
man/bb_annotate_npc.Rd
man/bb_blind_images.Rd
man/bb_buff_granges.Rd
man/bb_cds_anno.Rd
man/bb_cds_heatmap.Rd
man/bb_cellchat.Rd
man/bb_cellchat_heatmap.Rd
man/bb_cellmeta.Rd
man/bb_cite_umap.Rd
man/bb_cluster_representation.Rd
man/bb_cluster_representation2.Rd
man/bb_daseq.Rd
man/bb_doubletfinder.Rd
man/bb_extract_msig.Rd
man/bb_fix_file_path.Rd
man/bb_fragment_replacement.Rd
man/bb_gene_dotplot.Rd
man/bb_gene_modules.Rd
man/bb_gene_pseudotime.Rd
man/bb_gene_umap.Rd
man/bb_gene_violinplot.Rd
man/bb_genebubbles.Rd
man/bb_goenrichment.Rd
man/bb_goscatter.Rd
man/bb_gosummary.Rd
man/bb_import_bw.Rd
man/bb_import_seacr_peaks.Rd
man/bb_load_tenx_h5.Rd
man/bb_load_tenx_targz.Rd
man/bb_loupeR.Rd
man/bb_makeTrace.Rd
man/bb_make_ape_genomic.Rd
man/bb_make_ape_transcript.Rd
man/bb_merge_narrowpeaks.Rd
man/bb_metafeature.Rd
man/bb_monocle_.Rd
man/bb_monocle_regression.Rd
man/bb_monocle_regression_better.Rd
man/bb_parseape.Rd
man/bb_plot_genes_in_pseudotime.Rd
man/bb_plot_heatmap_colData.Rd
man/bb_plot_heatmap_colDendro.Rd
man/bb_plot_heatmap_colHighlight.Rd
man/bb_plot_heatmap_main.Rd
man/bb_plot_heatmap_rowData.Rd
man/bb_plot_heatmap_rowDendro.Rd
man/bb_plot_heatmap_rowHighlight.Rd
man/bb_plot_rowData_col.Rd
man/bb_plot_trace_axis.Rd
man/bb_plot_trace_data.Rd
man/bb_plot_trace_links.Rd
man/bb_plot_trace_model.Rd
man/bb_plot_trace_peaks.Rd
man/bb_plotfootprint.Rd
man/bb_print_full_stats.Rd
man/bb_promoter_overlap.Rd
man/bb_pseudobulk_mf.Rd
man/bb_pseudocells.Rd
man/bb_pseudotime.Rd
man/bb_qc.Rd
man/bb_read_bam.Rd
man/bb_read_narrowpeak.Rd
man/bb_rejoin.Rd
man/bb_remove_dupes.Rd
man/bb_rowmeta.Rd
man/bb_seurat_anno.Rd
man/bb_split_atac.Rd
man/bb_split_citeseq.Rd
man/bb_tbl_to_coldata.Rd
man/bb_tbl_to_matrix.Rd
man/bb_tbl_to_rowdata.Rd
man/bb_triplecluster.Rd
man/bb_unblind_images.Rd
man/bb_var_umap.Rd
man/dMcast.Rd
man/data_median_se.Rd
man/data_summary_mean_sd.Rd
man/data_summary_mean_se.Rd
man/data_summary_median_iqr.Rd
man/data_summary_median_mad.Rd
man/filter_cds.Rd
man/geom_split_violin.Rd
man/granges_to_features.Rd
man/grapes-notin-grapes.Rd
man/merge.Matrix.Rd
man/normalize_batch.Rd
man/rBind.fill.Rd
man/se.Rd
man/show-Ape-method.Rd
man/show-Trace-method.Rd
tests/testthat.R
tests/testthat/test-SummarizedHeatmap.R
vignettes/.gitignore
vignettes/Ape.Rmd
vignettes/SummarizedHeatmap.Rmd
vignettes/blind_images.Rmd
vignettes/scRNAseq.Rmd
vignettes/trace.Rmd
