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'))

Peer review:

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

On CRAN:

95 exports 1.58 score 401 dependencies

Last updated 1 months agofrom:4c6d9427f0

Exports:%notin%add_cds_factor_columnsApeApe.DNAApe.fastaApe.fimoApe.grangesApe.saveApe.setFeaturesbb_aggregatebb_alignbb_annotate_npcbb_blind_imagesbb_buff_grangesbb_cds_annobb_cds_heatmapbb_cellchatbb_cellchat_heatmapbb_cellmetabb_cite_umapbb_cluster_representationbb_cluster_representation2bb_doubletfinderbb_extract_msigbb_fix_file_pathbb_fragment_replacementbb_gene_dotplotbb_gene_modulesbb_gene_pseudotimebb_gene_umapbb_gene_violinplotbb_genebubblesbb_goenrichmentbb_goscatterbb_gosummarybb_load_tenx_h5bb_load_tenx_targzbb_make_ape_genomicbb_make_ape_transcriptbb_makeTracebb_metafeaturebb_monocle_regressionbb_monocle_regression_betterbb_parseapebb_plot_genes_in_pseudotimebb_plot_rowData_colbb_plot_trace_axisbb_plot_trace_databb_plot_trace_linksbb_plot_trace_modelbb_plot_trace_peaksbb_plotfootprintbb_print_full_statsbb_promoter_overlapbb_pseudobulk_mfbb_pseudotimebb_qcbb_read_bambb_read_narrowpeakbb_rejoinbb_remove_dupesbb_rowmetabb_seurat_annobb_split_atacbb_split_citeseqbb_tbl_to_coldatabb_tbl_to_matrixbb_tbl_to_rowdatabb_tripleclusterbb_unblind_imagesbb_var_umapCOMMENTSdata_median_sedata_summary_mean_sddata_summary_mean_sedata_summary_median_iqrdata_summary_median_madFEATURESfilter_cdsgeom_split_violingranges_to_featuresLOCUSnormalize_batchseshowTraceTrace.dataTrace.gene_modelTrace.linksTrace.peaksTrace.plot_rangeTrace.setDataTrace.setLinksTrace.setpeaksTrace.setRange

Dependencies:abindannotateAnnotationDbiashraskpassassertthatbackportsbase64encbatchelorbeachmatbeeswarmBHbiglmBiobaseBiocGenericsBiocIOBiocManagerBiocNeighborsBiocParallelBiocSingularBiostringsbitbit64bitopsblaseRdatablaseRtemplatesblobbootbrewbriobroomBSgenomeBSgenome.Drerio.UCSC.danRer11BSgenome.Hsapiens.UCSC.hg38bslibcachemCairocallrcarcarDatacaToolsCellChatcellrangercirclizeclassclassIntclicliprclueclustercodacodetoolscolorspacecommonmarkComplexHeatmapconflictedcorrplotcowplotcpp11crayoncredentialscrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdeldirdescDESeq2devtoolsdiffobjdigestdoParalleldotCall64DoubletFinderdownlitdplyrdqrngdtplyre1071edgeRellipsisetrunctevaluateexpmfansifarverfastDummiesfastmapfastmatchfieldsfilelockfitdistrplusFNNfontawesomeforcatsforeachformatRfsfurrrfutile.loggerfutile.optionsfuturefuture.applygarglegenefiltergeneplottergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgertGetoptLongggalluvialggbeeswarmggforceggnetworkggplot2ggpubrggrastrggrepelggridgesggsciggsignifggtextghgitcredsGlobalOptionsglobalsglueGO.dbgoftestgoogledrivegooglesheets4GOSemSimgplotsgraphgridBasegridExtragridtextgrrgtablegtoolshavenHDF5Arrayhdf5rherehexbinhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2huxtableicaidsigraphiniinvgammaIRangesirlbaisobanditeratorsjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenleidenbaselifecyclelimmalistenvlme4lmtestlocfitlubridatemagrittrmapsmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimeminiUIminqamixsqpmodelrmonocle3munsellnetworknlmenloptrNLPNMFnnetnumDerivopensslorg.Dr.eg.dborg.Hs.eg.dborg.Mm.eg.dbpakparallellypatchworkpbapplypbkrtestpbmcapplypheatmappillarpkgbuildpkgcachepkgconfigpkgdownpkgloadplogrplotlyplyrpngpolyclippolynompraiseprettyunitsprocessxprofvisprogressprogressrpromisespromptproxypspsclpurrrquantregR.methodsS3R.ooR.utilsR6raggRANNrappdirsrcmdcheckRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppRollRcppTOMLRCurlreadrreadxlregistryrematchrematch2remotesrenvreprexreshape2ResidualMatrixrestfulrreticulaterhdf5rhdf5filtersRhdf5libRhpcBLASctlRhtslibrjsonrlangrmarkdownrngtoolsROCRroxygen2rprojrootrrvgorsampleRsamtoolsRSpectraRSQLiterstatixrstudioapirsvdrtracklayerRtsnerversionsrvests2S4ArraysS4VectorssassScaledMatrixscalesscaterscattermoresctransformscuttleselectrsessioninfoSeuratSeuratDiskSeuratObjectsfshapeshinySignacSingleCellExperimentsitmoslamslidersnasnowsourcetoolsspspamSparseArraySparseMsparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.utilsspDataspdepspeedglmSQUAREMstatmodstatnet.commonstringistringrSummarizedExperimentsurvivalsvglitesyssystemfontstensortestthattextshapingtibbletidyrtidyselecttidyversetimechangetinytextmtopGOtreemaptruncnormtweenrTxDb.Drerio.UCSC.danRer11.ensGeneTxDb.Hsapiens.UCSC.hg38.knownGenetzdbUCSC.utilsumapunitsurlcheckerusethisutf8uuiduwotvctrsviporviridisviridisLitevroomwaldowarpwhiskerwithrwkwordcloudxfunXMLxml2xopenxtableXVectoryamlyulab.utilszipzlibbioczoo

Readme and manuals

Help Manual

Help pageTopics
blaseRtools: R Tools for Blaser Lab Data AnalysisblaseRtools-package SeuratWrappers-package blaseRtools
Operators%notin%
Add predefined sample-level cell metadata to cell data sets while importingadd_cds_factor_columns
Compute summary statistics of a Matrixaggregate.Matrix
An S4 class to hold genebank/APE file data.Ape Ape-class
Get the DNASringSet Slot from an Ape ObjectApe.DNA
Save an Ape Instance as a Fasta FileApe.fasta
Run FIMO on Selected Ape Object FeaturesApe.fimo
Get the GRanges Slot from an Ape ObjectApe.granges
Save an Ape Instance as a Genebank Format FileApe.save
Set the FEATURES Slot of a GRanges ObjectApe.setFeatures
Convert objects to Monocle3 'cell_data_set' objectsas.CellDataSet as.cell_data_set as.cell_data_set.Seurat
Convert single cell experiment to Seuratas.Seurat.cell_data_set
Aggregate Single Cell Gene Expressionbb_aggregate
Align a CDS object according to a metadata variablebb_align
Annotate a Plot using NPC Coordinatesbb_annotate_npc
Make a Copy of Image Files and Rename With File Hashes in Blinded Folderbb_blind_images
Clean Up Your GRanges Objectbb_buff_granges
Annotate a CDS by Label Transferbb_cds_anno
Make a Heatmap of Aggregated Gene Expressionf from a CDSbb_cds_heatmap
Infer Cell-Cell Communicationbb_cellchat
Make a Complex Heatmap From a CellChat Object With Sensible Defaultsbb_cellchat_heatmap
Get Cell Metadatabb_cellmeta
Plot a UMAP Showing Cite-Seq Antibody Bindingbb_cite_umap
Cluster Representation By Fisher Exact Test Per Cellbb_cluster_representation
Cluster Representation By Regression Per Samplebb_cluster_representation2
Use doubletfinder to model and mark doubletsbb_doubletfinder
Extract MSIGDB Gene Setsbb_extract_msig
Convert windows filepath to linux-compatible.bb_fix_file_path
Replace The Path to a Fragment File In a Signac Objectbb_fragment_replacement
Make a dotplot of gene expression by cell populationbb_gene_dotplot
A function to generate gene modules and add them to the Gene Metadatabb_gene_modules
Plot expression of a gene or genes in pseudotime.bb_gene_pseudotime
Make a Plot of Gene Expression in UMAP Formbb_gene_umap
Make a plot of gene expression in UMAP formbb_gene_violinplot
Create a Gene Bubble/Dot Plotbb_genebubbles
Go Term Enrichmentbb_goenrichment
Make a scatter plot of GO term associationsbb_goscatter
A function to reduce go terms by semantic similaritybb_gosummary
Load a 10X Genomics H5 File and Return a CDSbb_load_tenx_h5
Load 10X Data Into CDSbb_load_tenx_targz
Make an Ape Genome Objectbb_make_ape_genomic
Make an Ape Transcriptome Objectbb_make_ape_transcript
Construct a Trace object from a Signac Object or Granges objectbb_makeTrace
A Function To Merge Replicate Narrow Peaks GRangesbb_merge_narrowpeaks
A Function to Generate Data For Making MetaPlotsbb_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 Objectbb_parseape
Plots expression for one or more genes as a function of pseudotimebb_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 Objectbb_plot_trace_axis
Plot The Trace Data From A Trace Objectbb_plot_trace_data
Plot The Link Data From A Trace Objectbb_plot_trace_links
Plot The Gene Model From A Trace Objectbb_plot_trace_model
Plot The peak Data From A Trace Objectbb_plot_trace_peaks
Plot motif footprinting resultsbb_plotfootprint
Print out a stats reportbb_print_full_stats
Calculate The Overlap Between Peaks and Promotersbb_promoter_overlap
Run Multifactor Pseudobulk Analysis using Deseq2bb_pseudobulk_mf
Learn Graph and Calculate Pseudotimebb_pseudotime
A function to run qc tests on cds objects.bb_qc
Read Bam Filesbb_read_bam
A Function to Read In Narrow Peaks Filesbb_read_narrowpeak
Rejoin qc and doubletfinder data to a cds objectbb_rejoin
Remove rows that have duplicates in a given columnbb_remove_dupes
Get Feature/Gene Metadatabb_rowmeta
A function to generate automated cell labelings with Seuratbb_seurat_anno
Split Out Peaks Databb_split_atac
Split Antibody Capture Data into Alt Experimentbb_split_citeseq
A Function To Add Tibble Columns To Cell Metadatabb_tbl_to_coldata
Convert a wide-form tibble a matrixbb_tbl_to_matrix
A Function To Add Tibble Columns To Feature Metadatabb_tbl_to_rowdata
A function to generate clusters from scRNA-seq databb_triplecluster
Rejoin Blinded Scores to Original File Namesbb_unblind_images
A function to generate a UMAP with colors mapped to colData variablesbb_var_umap
Get the Comments Slot from an Ape ObjectCOMMENTS
Generate median +/- se stat object for jitter ggplotdata_median_se
Generate mean +/- sd stat object for jitter ggplotdata_summary_mean_sd
Generate mean +/- se stat object for jitter ggplotdata_summary_mean_se
Generate median +/- iqr stat object for jitter ggplotdata_summary_median_iqr
Generate median +/- mad stat object for jitter ggplotdata_summary_median_mad
Casts or pivots a long 'data frame' into a wide sparse matrixdMcast
Get the Features Slot from an Ape ObjectFEATURES
Filter a CDSfilter_cds
geom_split_violingeom_split_violin
Format a GRanges Object as a Character Vector For Inclusion in Genebank Filegranges_to_features
Run 'link[monocle3]{learn_graph}' on a 'Seurat' objectLearnGraph
Get the Locus Slot from an Ape ObjectLOCUS
Merges two Matrices or matrix-like objectsjoin.Matrix merge.Matrix
Noramalize a Data Table by Group and Batchnormalize_batch
Combine matrixes by row, fill in missing columnsrBind.fill
Calculate standard error of the meanse
Show an Ape Objectshow,Ape-method
Show a Trace Objectshow,Trace-method
An S4 class to Hold Genome Track DataTrace Trace-class
Get the Trace Data Slot from a Trace ObjectTrace.data
Get the gene_model Slot from a Trace ObjectTrace.gene_model
Get the Links Slot from a Trace ObjectTrace.links
Get the peaks Slot from a Trace ObjectTrace.peaks
Get the plot_range Slot from a Trace ObjectTrace.plot_range
Set the Trace Data Slot of a GRanges ObjectTrace.setData
Set the Links Slot of a GRanges ObjectTrace.setLinks
Set the peaks Slot of a GRanges ObjectTrace.setpeaks
Set the Plot Range Slot of a GRanges ObjectTrace.setRange