Package: blaseRtools 0.0.0.9163

blaseRtools: R Tools for Blaser Lab Data Analysis

This is a repository of R tools for Single Cell RNA seq and other lab data analysis functions.

Authors:Brad Blaser [aut, cre]

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blaseRtools.pdf |blaseRtools.html✨
blaseRtools/json (API)
NEWS

# Install 'blaseRtools' in R:

install.packages('blaseRtools', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org'))

The latest version of this package failed to build. Look at thebuild logs for more information.

Bug tracker:https://github.com/blaserlab/blasertools/issues

On CRAN:

95 exports 1.58 score 401 dependencies 6 scripts

Last updated 3 months agofrom:4c6d9427f0. Checks:OK: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Jun 14 2024

Exports:%notin%add_cds_factor_columns Ape Ape.DNA Ape.fasta Ape.fimo Ape.granges Ape.save Ape.setFeatures bb_aggregate bb_align bb_annotate_npc bb_blind_images bb_buff_granges bb_cds_anno bb_cds_heatmap bb_cellchat bb_cellchat_heatmap bb_cellmeta bb_cite_umap bb_cluster_representation bb_cluster_representation2 bb_doubletfinder bb_extract_msig bb_fix_file_path bb_fragment_replacement bb_gene_dotplot bb_gene_modules bb_gene_pseudotime bb_gene_umap bb_gene_violinplot bb_genebubbles bb_goenrichment bb_goscatter bb_gosummary bb_load_tenx_h5 bb_load_tenx_targz bb_make_ape_genomic bb_make_ape_transcript bb_makeTrace bb_metafeature bb_monocle_regression bb_monocle_regression_better bb_parseape bb_plot_genes_in_pseudotime bb_plot_rowData_col bb_plot_trace_axis bb_plot_trace_data bb_plot_trace_links bb_plot_trace_model bb_plot_trace_peaks bb_plotfootprint bb_print_full_stats bb_promoter_overlap bb_pseudobulk_mf bb_pseudotime bb_qc bb_read_bam bb_read_narrowpeak bb_rejoin bb_remove_dupes bb_rowmeta bb_seurat_anno bb_split_atac bb_split_citeseq bb_tbl_to_coldata bb_tbl_to_matrix bb_tbl_to_rowdata bb_triplecluster bb_unblind_images bb_var_umap COMMENTS data_median_se data_summary_mean_sd data_summary_mean_se data_summary_median_iqr data_summary_median_mad FEATURES filter_cds geom_split_violin granges_to_features LOCUS normalize_batch se show Trace Trace.data Trace.gene_model Trace.links Trace.peaks Trace.plot_range Trace.setData Trace.setLinks Trace.setpeaks Trace.setRange

Dependencies:abind annotate AnnotationDbi ashr askpass assertthat backports base64enc batchelor beachmat beeswarm BH biglm Biobase BiocGenerics BiocIO BiocManager BiocNeighbors BiocParallel BiocSingular Biostrings bit bit64 bitops blaseRdata blaseRtemplates blob boot brew brio broom BSgenome BSgenome.Drerio.UCSC.danRer11 BSgenome.Hsapiens.UCSC.hg38 bslib cachem Cairo callr car carData caTools CellChat cellranger circlize class classInt cli clipr clue cluster coda codetools colorspace commonmark ComplexHeatmap conflicted corrplot cowplot cpp11 crayon credentials crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir desc DESeq2 devtools diffobj digest doParallel dotCall64 DoubletFinder downlit dplyr dqrng dtplyr e1071 edgeR ellipsis etrunct evaluate expm fansi farver fastDummies fastmap fastmatch fields filelock fitdistrplus FNN fontawesome forcats foreach formatR fs furrr futile.logger futile.options future future.apply gargle genefilter geneplotter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges gert GetoptLong ggalluvial ggbeeswarm ggforce ggnetwork ggplot2 ggpubr ggrastr ggrepel ggridges ggsci ggsignif ggtext gh gitcreds GlobalOptions globals glue GO.db goftest googledrive googlesheets4 GOSemSim gplots graph gridBase gridExtra gridtext grr gtable gtools haven HDF5Array hdf5r here hexbin highr hms htmltools htmlwidgets httpuv httr httr2 huxtable ica ids igraph ini invgamma IRanges irlba isoband iterators jpeg jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval leiden leidenbase lifecycle limma listenv lme4 lmtest locfit lubridate magrittr maps markdown MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime miniUI minqa mixsqp modelr monocle3 munsell network nlme nloptr NLP NMF nnet numDeriv openssl org.Dr.eg.db org.Hs.eg.db org.Mm.eg.db pak parallelly patchwork pbapply pbkrtest pbmcapply pheatmap pillar pkgbuild pkgcache pkgconfig pkgdown pkgload plogr plotly plyr png polyclip polynom praise prettyunits processx profvis progress progressr promises prompt proxy ps pscl purrr quantreg R.methodsS3 R.oo R.utils R6 ragg RANN rappdirs rcmdcheck RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppML RcppProgress RcppRoll RcppTOML RCurl readr readxl registry rematch rematch2 remotes renv reprex reshape2 ResidualMatrix restfulr reticulate rhdf5 rhdf5filters Rhdf5lib RhpcBLASctl Rhtslib rjson rlang rmarkdown rngtools ROCR roxygen2 rprojroot rrvgo rsample Rsamtools RSpectra RSQLite rstatix rstudioapi rsvd rtracklayer Rtsne rversions rvest s2 S4Arrays S4Vectors sass ScaledMatrix scales scater scattermore sctransform scuttle selectr sessioninfo Seurat SeuratDisk SeuratObject sf shape shiny Signac SingleCellExperiment sitmo slam slider sna snow sourcetools sp spam SparseArray SparseM sparseMatrixStats spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.utils spData spdep speedglm SQUAREM statmod statnet.common stringi stringr SummarizedExperiment survival svglite sys systemfonts tensor testthat textshaping tibble tidyr tidyselect tidyverse timechange tinytex tm topGO treemap truncnorm tweenr TxDb.Drerio.UCSC.danRer11.ensGene TxDb.Hsapiens.UCSC.hg38.knownGene tzdb UCSC.utils umap units urlchecker usethis utf8 uuid uwot vctrs vipor viridis viridisLite vroom waldo warp whisker withr wk wordcloud xfun XML xml2 xopen xtable XVector yaml yulab.utils zip zlibbioc zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
blaseRtools: R Tools for Blaser Lab Data Analysis	blaseRtools-package SeuratWrappers-package blaseRtools
Operators	%notin%
Add predefined sample-level cell metadata to cell data sets while importing	add_cds_factor_columns
Compute summary statistics of a Matrix	aggregate.Matrix
An S4 class to hold genebank/APE file data.	Ape Ape-class
Get the DNASringSet Slot from an Ape Object	Ape.DNA
Save an Ape Instance as a Fasta File	Ape.fasta
Run FIMO on Selected Ape Object Features	Ape.fimo
Get the GRanges Slot from an Ape Object	Ape.granges
Save an Ape Instance as a Genebank Format File	Ape.save
Set the FEATURES Slot of a GRanges Object	Ape.setFeatures
Convert objects to Monocle3 'cell_data_set' objects	as.CellDataSet as.cell_data_set as.cell_data_set.Seurat
Convert single cell experiment to Seurat	as.Seurat.cell_data_set
Aggregate Single Cell Gene Expression	bb_aggregate
Align a CDS object according to a metadata variable	bb_align
Annotate a Plot using NPC Coordinates	bb_annotate_npc
Make a Copy of Image Files and Rename With File Hashes in Blinded Folder	bb_blind_images
Clean Up Your GRanges Object	bb_buff_granges
Annotate a CDS by Label Transfer	bb_cds_anno
Make a Heatmap of Aggregated Gene Expressionf from a CDS	bb_cds_heatmap
Infer Cell-Cell Communication	bb_cellchat
Make a Complex Heatmap From a CellChat Object With Sensible Defaults	bb_cellchat_heatmap
Get Cell Metadata	bb_cellmeta
Plot a UMAP Showing Cite-Seq Antibody Binding	bb_cite_umap
Cluster Representation By Fisher Exact Test Per Cell	bb_cluster_representation
Cluster Representation By Regression Per Sample	bb_cluster_representation2
Use doubletfinder to model and mark doublets	bb_doubletfinder
Extract MSIGDB Gene Sets	bb_extract_msig
Convert windows filepath to linux-compatible.	bb_fix_file_path
Replace The Path to a Fragment File In a Signac Object	bb_fragment_replacement
Make a dotplot of gene expression by cell population	bb_gene_dotplot
A function to generate gene modules and add them to the Gene Metadata	bb_gene_modules
Plot expression of a gene or genes in pseudotime.	bb_gene_pseudotime
Make a Plot of Gene Expression in UMAP Form	bb_gene_umap
Make a plot of gene expression in UMAP form	bb_gene_violinplot
Create a Gene Bubble/Dot Plot	bb_genebubbles
Go Term Enrichment	bb_goenrichment
Make a scatter plot of GO term associations	bb_goscatter
A function to reduce go terms by semantic similarity	bb_gosummary
Load a 10X Genomics H5 File and Return a CDS	bb_load_tenx_h5
Load 10X Data Into CDS	bb_load_tenx_targz
Make an Ape Genome Object	bb_make_ape_genomic
Make an Ape Transcriptome Object	bb_make_ape_transcript
Construct a Trace object from a Signac Object or Granges object	bb_makeTrace
A Function To Merge Replicate Narrow Peaks GRanges	bb_merge_narrowpeaks
A Function to Generate Data For Making MetaPlots	bb_metafeature
A function to perform regression on single cell data.	bb_monocle_regression
An Improved Function to Perform Regression on Single Cell Data.	bb_monocle_regression_better
Parse a Genebank File and Construct an APE Object	bb_parseape
Plots expression for one or more genes as a function of pseudotime	bb_plot_genes_in_pseudotime
A helper function to generate a data frame in the proper form for aggregate expression plotting with bb_gene_umap.	bb_plot_rowData_col
Plot The X Axis From A Trace Object	bb_plot_trace_axis
Plot The Trace Data From A Trace Object	bb_plot_trace_data
Plot The Link Data From A Trace Object	bb_plot_trace_links
Plot The Gene Model From A Trace Object	bb_plot_trace_model
Plot The peak Data From A Trace Object	bb_plot_trace_peaks
Plot motif footprinting results	bb_plotfootprint
Print out a stats report	bb_print_full_stats
Calculate The Overlap Between Peaks and Promoters	bb_promoter_overlap
Run Multifactor Pseudobulk Analysis using Deseq2	bb_pseudobulk_mf
Learn Graph and Calculate Pseudotime	bb_pseudotime
A function to run qc tests on cds objects.	bb_qc
Read Bam Files	bb_read_bam
A Function to Read In Narrow Peaks Files	bb_read_narrowpeak
Rejoin qc and doubletfinder data to a cds object	bb_rejoin
Remove rows that have duplicates in a given column	bb_remove_dupes
Get Feature/Gene Metadata	bb_rowmeta
A function to generate automated cell labelings with Seurat	bb_seurat_anno
Split Out Peaks Data	bb_split_atac
Split Antibody Capture Data into Alt Experiment	bb_split_citeseq
A Function To Add Tibble Columns To Cell Metadata	bb_tbl_to_coldata
Convert a wide-form tibble a matrix	bb_tbl_to_matrix
A Function To Add Tibble Columns To Feature Metadata	bb_tbl_to_rowdata
A function to generate clusters from scRNA-seq data	bb_triplecluster
Rejoin Blinded Scores to Original File Names	bb_unblind_images
A function to generate a UMAP with colors mapped to colData variables	bb_var_umap
Get the Comments Slot from an Ape Object	COMMENTS
Generate median +/- se stat object for jitter ggplot	data_median_se
Generate mean +/- sd stat object for jitter ggplot	data_summary_mean_sd
Generate mean +/- se stat object for jitter ggplot	data_summary_mean_se
Generate median +/- iqr stat object for jitter ggplot	data_summary_median_iqr
Generate median +/- mad stat object for jitter ggplot	data_summary_median_mad
Casts or pivots a long 'data frame' into a wide sparse matrix	dMcast
Get the Features Slot from an Ape Object	FEATURES
Filter a CDS	filter_cds
geom_split_violin	geom_split_violin
Format a GRanges Object as a Character Vector For Inclusion in Genebank File	granges_to_features
Run 'link[monocle3]{learn_graph}' on a 'Seurat' object	LearnGraph
Get the Locus Slot from an Ape Object	LOCUS
Merges two Matrices or matrix-like objects	join.Matrix merge.Matrix
Noramalize a Data Table by Group and Batch	normalize_batch
Combine matrixes by row, fill in missing columns	rBind.fill
Calculate standard error of the mean	se
Show an Ape Object	show,Ape-method
Show a Trace Object	show,Trace-method
An S4 class to Hold Genome Track Data	Trace Trace-class
Get the Trace Data Slot from a Trace Object	Trace.data
Get the gene_model Slot from a Trace Object	Trace.gene_model
Get the Links Slot from a Trace Object	Trace.links
Get the peaks Slot from a Trace Object	Trace.peaks
Get the plot_range Slot from a Trace Object	Trace.plot_range
Set the Trace Data Slot of a GRanges Object	Trace.setData
Set the Links Slot of a GRanges Object	Trace.setLinks
Set the peaks Slot of a GRanges Object	Trace.setpeaks
Set the Plot Range Slot of a GRanges Object	Trace.setRange