Package index • Zorn

All functions

AggregateMinhashes(): Aggregate frequency of minhashes across cells
AtrandiBarcodeStats(): Given a Bascet, produce a matrix showing for each combinatorial barcode, how many times it occurs across the cells. Presented as a 96-well plate matrix
BarnyardPlotMatrix(): Produce a matrix of Barnyard plots, i.e., counts for one species vs another, for all combinations of species.
Bascet-class: A bascet, along with all the shards
BascetAddMetaData(): Add metadata to a Seurat object, handling cell mismatches
BascetAggregateAMRfinder(): Aggregate data from AMRfinder This is a thin wrapper around BascetAggregateMap
BascetAggregateAbricate(): Aggregate data from Abricate This is a thin wrapper around BascetAggregateMap
BascetAggregateAriba(): Aggregate data from Ariba This is a thin wrapper around BascetAggregateMap
BascetAggregateFASTQC(): Aggregate data from FASTQC This is a thin wrapper around BascetAggregateMap
BascetAggregateGECCO(): Aggregate data from GECCO This is a thin wrapper around BascetAggregateMap
BascetAggregateMap(): Aggregate data from previous Map call
BascetAggregateQUAST(): Aggregate data from QUAST This is a thin wrapper around BascetAggregateMap
BascetAlignToReference(): Align from FASTQ, generate sorted and indexed BAM file
BascetAlignmentToBigwig(): Generate a bigwig out of all reads in a sorted BAM. Note that the caller is responsible for sorting the BAM first
BascetBam2Fragments(): Take aligned BAM file and produce Fragments.tsv.gz, compatible with Signac ATAC-seq style analysis
BascetCacheComputation(): A wrapper to cache a computation. Put your function in as an argument, as R will only compute its value if needed. If the cache file exist, it will not be run again
BascetCellNames(): Get list of cells in a Bascet
BascetComputeMinhash(): Compute minhashes for each cell. This is a thin wrapper around BascetMapCell
BascetCountChrom(): From aligned BAM file, compute counts per chromosome
BascetCountFeature(): From aligned BAM file, compute counts per feature
BascetCountMatrixToAssay(): Convert a BascetCountMatrix to a Seurat Assay
BascetDebarcode(): Extract barcodes and trim input raw FASTQ
BascetDownloadNcbiGenomeMetadata(): Download and cache an NCBI genome assembly summary
BascetDownloadNcbiGenomes(): Download sharded NCBI genome inputs into Bascet files
BascetDownloadSraRuns(): Download sharded SRA run lists into Bascet TIRP files
BascetDumpContigs(): Store all contigs in an output directory, as cell_id.fa
BascetFilterAlignment(): Filter an alignment (BAM-file).
BascetIndexGenomeBWAMEM2(): Index a genome using BWA-MEM2 such that it can be used for alignment
BascetIndexGenomeBowtie2(): Index a genome using Bowtie2 such that it can be used for alignment
BascetIndexGenomeMinimap2(): Index a genome using minimap2 such that it can be used for alignment
BascetIndexGenomeSTAR(): Index a genome using STAR such that it can be used for alignment. Note that Bascet STAR (star-rs) automatically detects if GTF and FASTA are gzipped
BascetInstance(): Create a new bascet instance. For advanced users only
BascetListFilesForCell(): List files for a cell in a Bascet
BascetLoadCountSketchMatrix(): Load count sketch matrix as Seurat object
BascetMakeMinhashHistogram(): Gather all minhashes into a single histogram file
BascetMapCell(): Call a MAP function for all cells
BascetMapCellAMRfinder(): Run AMRfinder on contigs of all cells. This is a thin wrapper around BascetMapCell
BascetMapCellAbricate(): Run Abricate on contigs of all cells. This is a thin wrapper around BascetMapCell
BascetMapCellAriba(): Run Ariba on reads of all cells. This is a thin wrapper around BascetMapCell
BascetMapCellBakta(): Run Bakta on contigs of all cells. This is a thin wrapper around BascetMapCell
BascetMapCellFASTQC(): Run FASTQC on reads of all cells.
BascetMapCellGECCO(): Run GECCO on contigs of all cells.
BascetMapCellQUAST(): Run QUAST on reads of all cells. This is a thin wrapper around BascetMapCell
BascetMapCellSKESA(): Run integrated SKESA on reads from each cell.
BascetMapTransform(): Transform data
BascetPrepareNcbiGenomeFetchLists(): Write sharded NCBI genome download inputs
BascetPrepareSraFetchLists(): Write sharded SRA accession lists for later import
BascetQueryFq(): Build count table from FASTQ reads and a list of selected kmers
BascetReadFile(): Read one file from a Bascet
BascetReadMinhashHistogram(): Read histogram of KMERs, the output of BascetMakeMinhashHistogram
BascetReadNcbiGenomeMetadata(): Read cached NCBI genome assembly metadata
BascetResolveSra(): Resolve SRA inputs to a canonical run table
BascetRunCellSNP(): Align from FASTQ, generate sorted and indexed BAM file
BascetRunCountsketch(): Gather all count sketches into a single count sketch matrix
BascetRunFASTP(): Run FASTP for each cell. Input must be in FASTQ file format
BascetRunKraken(): Run KRAKEN2 for each cell. Then produce a count matrix of taxonomy IDs from the output
BascetShardify(): Take debarcoded reads, merge them, and split them into suitable numbers of shards.
BascetToFastq(): Convert data to Bascet-FASTQ
ChooseInformativeKMERs(): Pick random KMERs from KMC3 database. The choice is among KMERs within a frequency range
ChromToSpeciesCount(): Produce a count matrix on strain level
CloseBascet(): Close a Bascet file.
CountDataFrameToSparseMatrix(): Count entries in long format data frame and return as a sparse matrix
CountGrangeFeatures(): Obtain a feature matrix (as seurat object) given an seurat object having Fragments associated
CountSketchUMAP(): Run UMAP on a count sketch reduction
CreateSeuratObject.BascetCountMatrix(): Create a Seurat object from a BascetCountMatrix
CreateSeuratObjectWithReduction(): Create a seurat object from e.g. count sketch reduction
DebarcodedKneePlot(): Produce summary kneeplot given debarcoded statistics
DetectRawFileMeta(): Detect metadata for raw input FASTQ files
DownloadDatabaseAMRfinder(): Download a database for AMRfinder
DownloadDatabaseAriba(): Download database for Ariba
DownloadDatabaseBakta(): Download a database for Bakta
FragmentCountsPerChrom(): From a Signac chromatin assay with fragments, for each cell, count how many reads per chromosome
FragmentCountsPerChromAssay(): From a Signac chromatin assay with fragments, for each cell, count how many reads per chromosome. This function directly returns an assay that can be added to a Seurat multimodal object
FragmentsToSignac(): From a fragments file, get a chromatin assay for Signac.
GetBascetTempDir(): Get a temp directory to use; need to be created
GetDefaultBascetInstance(): Get default Bascet instance from global variable (bascetInstance.default)
GetDefaultBascetRunner(): Get the current default runner
GetFASTQCassembledDF(): Get a data frame for one type of FASTQ statistics across across all cells
GetFASTQCbasicStats(): From aggregated FASTQC data, get basic statistics for overlay on UMAP etc
GetFASTQCpassfailStats(): From aggregated FASTQC data, get overall pass-fail statistics for overlay on UMAP etc
KneeplotPerSpecies(): Produce a kneeplot
KrakenFindConsensusTaxonomy(): For a KRAKEN2 count matrix, return consensus taxID for each cell as metadata
KrakenKneePlot(): Take a KRAKEN2 adata object and generate per-species kneeplots
KrakenSpeciesDistribution(): Using a KRAKEN2 count matrix, produce a "kneeplot" of species
ListDatabaseAbricate(): List installed databases available for Abricate
LocalRunner(): Create new local runner instance
MapCellMultiListAsDataFrame(): Convenience function; alternative is to somehow implement as.data.frame
MapListAsDataFrame(): Convenience function; alternative is to somehow implement as.data.frame.
MergeBascetCountMatrix(): Merge a list of count matrices as produced by Bascet
NoRunner(): Create new no-runner instance, used for debugging
OpenBascet(): Open a Bascet, prepare it for reading individual files
PlotFASTQCadapterContent(): From aggregated FASTQC data, plot adapter content
PlotHistogram(): Plot a histogram, loaded by ReadHistogram
PlotJohnsonLindenstraussMinDim(): Plot minimum number of dimensions needed to retain distance between samples
PrepareSharding(): Prepare to shard reads by collecting statistics about each barcode, and filtering out cells with few reads
ReadBascetCountMatrix(): Read a count matrix as produced by Bascet (hdf5 format). This can be output from both BascetQueryFq and BascetCountChrom
ReadCellSNPmatrix(): Read a count matrix as produced by CellSNP, but as shards
ReadHistogram(): Read the count histogram associated with a Bascet. Not all Bascets have one, but it is typically produced after debarcoding
ShowFASTQCforCell(): Show the FASTQC HTML report for a cell, in the available web browser
SlurmRunner(): Create a runner that submits jobs to SLURM
TabixGetFragmentsSeqs(): Using Tabix, get list of sequences in a fragment file
TestBascetInstance(): Check if a Bascet instance works
aggr.abricate(): Callback function for aggregating ABRicate data for each cell. To be called from BascetAggregateMap
aggr.amrfinder(): Callback function for aggregating ABRicate data for each cell. To be called from BascetAggregateMap
aggr.ariba(): Callback function for aggregating ARIBA data for each cell. To be called from BascetAggregateMap
aggr.fastqc(): Callback function for aggregating FASTQC data for each cell. To be called from BascetAggregateMap
aggr.gecco(): Callback function for aggregating GECCO data for each cell. To be called from BascetAggregateMap
aggr.minhash(): Callback function for aggregating min-hashes for each cell. To be called from BascetAggregateMap
aggr.quast(): Callback function for aggregating QUAST data. To be called from BascetAggregateMap
aggr.rawtext(): Callback function for just getting raw file contents To be called from BascetAggregateMap
colSums(<BascetCountMatrix>): Column sums of a BascetCountMatrix (counts per feature)
colnames(<BascetCountMatrix>): Column names of a BascetCountMatrix (feature names)
`colnames<-`(<BascetCountMatrix>): Set column names of a BascetCountMatrix (feature names)
createSlurmJobFromExisting(): This creates a job object, linking to a running command. Mainly used for development but can be used in case a Zorn session died and you want to create a new monitor
defaultBascetBinDir(): Get the default directory for storing Bascet binaries
dim(<BascetCountMatrix>): Dimensions of a BascetCountMatrix
formatPlainNumber(): Parse a string with a size, such as 1g, 1m, 1k, or just 123 (bytes)
getBascetBinary(): Get a Bascet binary for the current platform It will be cached in the provided directory to avoid downloading it each the time the function is called
getBascetDevDir(): Get a Bascet binary from the target from a locally built Bascet repository
is.BascetCountMatrix(): Check that parameter is a BascetCountMatrix
isBamPairedAlignment(): Figure out if a BAM-file is a paired alignment or not
lseq(): logarithmic spaced sequence; taken from emdbook library
rowSums(<BascetCountMatrix>): Row sums of a BascetCountMatrix (counts per cell)
rownames(<BascetCountMatrix>): Row names of a BascetCountMatrix (cell names)
`rownames<-`(<BascetCountMatrix>): Set row names of a BascetCountMatrix (cell names)
`[`(<BascetCountMatrix>,<ANY>,<ANY>,<ANY>): Subset a BascetCountMatrix