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
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
BascetCellNames_withstreamer(): Get list of cells in a Bascet – streamer provided
BascetComputeCountSketch(): Compute count sketch for each cell. This is a thin wrapper around BascetMapCell
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
BascetDumpContigs(): Store all contigs in an output directory, as cell_id.fa
BascetFilterAlignment(): Filter an alignment (BAM-file).
BascetGatherCountSketch(): Gather all count sketches into a single count sketch matrix
BascetGetRaw(): Extract barcodes and trim input raw FASTQ
BascetIndexGenomeBWA(): Index a genome using BWA such that it can be used for alignment
BascetIndexGenomeSTAR(): Index a genome using STAR such that it can be used for alignment
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
BascetMakeKrakenCountMatrix(): Produce a count matrix of taxonomy IDs from KRAKEN output
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. This is a thin wrapper around BascetMapCell
BascetMapCellGECCO(): Run GEECCO on contigs of all cells. This is a thin wrapper around BascetMapCell
BascetMapCellQUAST(): Run QUAST on reads of all cells. This is a thin wrapper around BascetMapCell
BascetMapTransform(): Transform data
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
BascetRunCellSNP(): Align from FASTQ, generate sorted and indexed BAM file
BascetRunFASTP(): Run FASTP for each cell. Input must be in FASTQ file format
BascetRunKraken(): Run KRAKEN2 for each cell
BascetShardify(): Take debarcoded reads, merge them, and split them into suitable numbers of shards.
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
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.
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
SetTaxonomyNamesFeatures(): Take a KRAKEN2 count matrix where the column is the taxonomyID. Convert to a matrix where the columns instead are the names of each taxonomy. Unused taxonomyID columns will not be kept
ShowFASTQCforCell(): Show the FASTQC HTML report for a cell, in the available web browser
SlurmRunner(): Create a runner that submits jobs to SLURM
SpeciesCorrMatrix(): TODO is this function used? export
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
assembleBascetCommand(): Prepare Bascet command given arguments
bascetCheckOverwriteOutput(): Detect metadata for raw input FASTQ files
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
detectShardsForFile(): Helper function: Figure out which shards belong together given root input name and extension i.e. root/name.##.ext
extractstreamerExit(): extract streamer: end an instance. the object should no longer be used after calling this function
extractstreamerExtractTo(): extract streamer: extract to external file
extractstreamerListCellsAnyFile(): extract streamer: list all cells in a given file
extractstreamerLs(): extract streamer: list all files in current Bascet zip-file
extractstreamerOpen(): extract streamer: set which file is open
extractstreamerReadNLines(): extract streamer: helper function to read N lines
extractstreamerReadOneLine(): extract streamer: helper function to read one line
extractstreamerShowtext(): extract streamer: get content of file, assumed to be text (or this function crashes)
extractstreamerStart(): extract streamer: create an instance
getBascetDockerImage(): Get and install a Bascet docker image. It will be cached to avoid downloading it each the time the function is called
getBascetSingularityImage(): Get a Bascet image (singularity or docker). It will be cached in the provided directory to avoid downloading it each the time the function is called
getFastqR2fromR1(): Get corresponding R2 file. Assumes that the input file is R1
is.bascet.file(): Check that parameter is a valid bascet file
is.bascet.instance(): Check that parameter is a valid bascet instance
is.existing.fasta(): Check that parameter is a valid shard name
is.integer.like(): Check that parameter is castable to an integer
is.numeric(<range01>): Check that parameter is a number between 0..1
is.positive.integer(): Check that parameter is an integer and >0
is.runner(): Check that parameter is a valid runner
is.streamer(): Check that parameter is a valid streamer
is.valid.env.variable(): Check that parameter is a valid environment variable name
is.valid.listcells(): Check that parameter is a valid list of cells
is.valid.shardname(): Check that parameter is a valid shard name
is.valid.threadcount(): Check that parameter is a valid thread count
isBamPairedAlignment(): Figure out if a BAM-file is a paired alignment or not
isFastq(): Check if a file is a FASTQ file
isPairedFastq(): Check if a file is a paired FASTQ file. Panics if the file is not a FASTQ at all
lseq(): logarithmic spaced sequence; taken from emdbook library
makeOutputShardNames(): Helper function: Generate suitable output filenames according to shard system i.e. root/name.##.ext
new_no_job(): Create an empty job. It is considered to have terminated from the start
parse_size_to_bytes(): Parse a string with a size, such as 1g, 1m, 1k, or just 123 (bytes)
removeBascetDockerImage(): Remove current Bascet docker image
safeDownloadMD5(): Download a file, check MD5 to ensure success. This assumes a file.md5 is stored on the server
shellscriptCancelJobIfFileExists(): Create a piece of script to exit a job early if file exists
shellscriptMakeBashArray(): Helper function: Create array of values in bash scripts example: myArray=("cat" "dog" "mouse" "frog")
shellscriptMakeCommalist(): Helper function, taking a list of elements such as a,b, and returning "a,b"
shellscriptMakeFilesExpander(): Generate a shell script command to produce a file of list of strings
shellscriptMakeOneFileExpander(): Helper function that takes content of a list and generates a BASH script that stores the content in a temporary file during execution
shellscriptSplitArrayIntoListRandomly(): Helper function to take an array of elements and split it randomly into a number of subset lists