Package: chevreulProcess 0.99.21

chevreulProcess: Tools for managing SingleCellExperiment objects as projects

Tools analyzing SingleCellExperiment objects as projects. for input into the Chevreul app downstream. Includes functions for analysis of single cell RNA sequencing data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

Authors:Kevin Stachelek [aut, cre], Bhavana Bhat [aut]

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

# Install 'chevreulProcess' in R:
install.packages('chevreulProcess', repos = c('https://whtns.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/cobriniklab/chevreulprocess/issues

Datasets:

On CRAN:

coveragernaseqsequencingvisualizationgeneexpressiontranscriptionsinglecelltranscriptomicsnormalizationpreprocessingqualitycontroldimensionreductiondataimport

2.30 score 2 scripts 22 exports 187 dependencies

Last updated 5 days agofrom:2c1dbd1864. Checks:ERROR: 1 WARNING: 4. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 18 2024
R-4.5-winWARNINGNov 18 2024
R-4.5-linuxWARNINGNov 18 2024
R-4.4-winWARNINGNov 18 2024
R-4.4-macWARNINGNov 18 2024

Exports:find_all_markersgenes_to_transcriptsget_colDataget_feature_typesget_featuresget_variable_featuresintegration_workflowload_bigwigspropagate_spreadsheet_changesquery_experimentrecord_experiment_dataregress_cell_cyclereintegrate_scesce_calcnsce_clustersce_desce_integratesce_processset_colDataset_feature_typesplitByColtranscripts_to_genes

Dependencies:abindAnnotationDbiAnnotationFilteraskpassassortheadbatchelorbeachmatbeeswarmBHBiobaseBiocGenericsBiocIOBiocNeighborsBiocParallelBiocSingularBiostringsbitbit64bitopsblobblusterbriocachemCairocallrcirclizeclicliprclustercmdfuncodetoolscolorspacecpp11crayoncredentialscurlDBIDelayedArrayDelayedMatrixStatsdescdiffobjdigestdplyrdqrngedgeREnsDb.Hsapiens.v86ensembldbevaluatefansifarverfastmapFNNformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgertggbeeswarmggplot2ggrastrggrepelghgitcredsGlobalOptionsgluegridExtragtablehmshttrhttr2igraphiniIRangesirlbaisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmegadepthmemoisemetapodmgcvmimemunsellnlmeopensslpheatmappillarpkgbuildpkgconfigpkgloadplogrpngpraiseprettyunitsprocessxprogressProtGenericspspurrrR.methodsS3R.ooR.utilsR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressRCurlreadrResidualMatrixrestfulrRhtslibrjsonrlangrprojrootRsamtoolsRSpectraRSQLiterstudioapirsvdrtracklayerRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscranscuttleshapeSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsyssystemfontstestthattextshapingtibbletidyrtidyselecttzdbUCSC.utilsusethisutf8uwotvctrsviporviridisviridisLitevroomwaldowhiskerwithrxfunXMLXVectoryamlzipzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Annotate percent mitochondrial reads per celladd_percent_mito
Annotate Cell Cycleannotate_cell_cycle
Update a database of chevreul projectsappend_to_project_db
Create a database of bigwigfilesbuild_bigwig_db
Cyclone cell cycle pairs by symbolcc.genes.cyclone
Clustering Workflowclustering_workflow
Convert SingleCellExperiment Objects from Human to Mouseconvert_human_sce_to_mouse
Convert gene symbols between mouse and humanconvert_symbols_by_species
Create a database of chevreul projectscreate_project_db
Ensembl version used for buildensembl_version
Find All Markersfind_all_markers
Gene Symbols to Ensembl Transcript Idsgenes_to_transcripts
Get cell metadata from a given objectget_colData
Get Feature Typesget_feature_types
Get feature namesget_features
Get object metadataget_sce_metadata
Get Transcripts in objectget_transcripts_from_sce
Get variable featuresget_variable_features
Human annotation datagrch38
Human transcripts to genesgrch38_tx2gene
Gene Homologs Between Human and Mousehuman_to_mouse_homologs
Batch Correct Multiple Single Cell Objectsintegrate
Integration Workflowintegration_workflow
Load Bigwigsload_bigwigs
Load SingleCellExperiment Files from a single project pathload_sce_from_proj
Read in Gene and Transcript SingleCellExperiment Objectsload_sce_path
Make Bigwig Databasemake_bigwig_db
Merge Small SingleCellExperiment Objectsmerge_small_sces
Retrieve Metadata from Batchmetadata_from_batch
Propagate Metadata Changespropagate_spreadsheet_changes
Query Experimentquery_experiment
Read a database of chevreul projectsread_project_db
Record Experiment Metadatarecord_experiment_data
Regress SingleCellExperiment Object by Given Set of Genesregress_cell_cycle
Reintegrate (filtered) SingleCellExperiment objectsreintegrate_sce
Retrieve Assayretrieve_experiment
Save object to /output/sce/_sce.rdssave_sce
Calculate Read Count Metrics for a objectsce_calcn
Run Louvain Clustering at Multiple Resolutionssce_cluster
Run Differential Expressionsce_de
Run SingleCellExperiment Integrationsce_integrate
Preprocess Single Cell Objectsce_preprocess
Run SingleCellExperiment Pipelinesce_process
Dimensional Reductionsce_reduce_dimensions
Set cell metadataset_colData
Set Feature Typesset_feature_type
Small example SingleCellExperimentsmall_example_dataset
Split SingleCellExperiment by colData variablesplitByCol
Stash Marker Genes in a SingleCellExperiment Objectstash_marker_features
Subset by new colDatasubset_by_colData
Tiny example SingleCellExperimenttiny_sce
Ensembl Transcript Ids to Gene Symbolstranscripts_to_genes
Update a database of chevreul projectsupdate_project_db