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

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

BascetFeaturiseKMC(): Select kmers that appear useful for clustering

BascetFilterAlignment(): Filter an alignment (BAM-file).

BascetGatherCountSketch(): Gather all count sketches into a single count sketch matrix

BascetGetRaw(): Generate BAM with barcodes from 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

BascetQueryKMC(): Build count table from kmer table and a list of selected kmers

BascetReadFile(): Read one file from a Bascet

BascetReadMinhashHistogram(): Read histogram of KMERs, the output of BascetMakeMinhashHistogram

BascetRunFASTP(): Run FASTP for each cell. Input must be in FASTQ file format

BascetRunKraken(): Run KRAKEN2 for each cell

BascetShardify(): Take debarcoded reads 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

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 .......................... signac is dirt slow at counting! only 1 cpu used. take over the whole process

GetBascetTempDir(): Get a temp directory to use; need to be created

GetDefaultBascetInstance(): Get Bascet instance from global variable

GetFASTQCassembledDF(): Get a data frame for one type of FASTQ statistics across across all cells

GetFASTQCpassfailStats(): From aggregated FASTQC data, get overall statistics for overlay on UMAP etc

KmcChooseKmerFeatures(): Pick random KMERs from KMC3 database. The choice is among KMERs within a frequency range

KmcGetHistogram(): Generate a histogram from a KMC3 database

KmcGetKmers(): Get KMERs from a KMC3 database

KneeplotPerSpecies(): Produce a kneeplot

KrakenFindConsensusTaxonomy(): For a KRAKEN2 count matrix, return consensus taxID for each cell as metadata

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

ReadBascetCountMatrix(): Read a count matrix as produced by Bascet (hdf5 format). This can be output from both BascetQueryFq and BascetCountChrom

ReadBascetKrakenMatrix(): Read a KRAKEN2 count matrix as produced by Bascet (hdf5 format)

ReadBascetKrakenMatrix_one(): Internal function, to load a single kraken matrix

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

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

bascet_check_overwrite_output(): Detect metadata for raw input FASTQ files

bascet_instance.default: The default Bascet installation settings

detect_shards_for_file(): Helper function: Figure out which shards belong together given root input name and extension i.e. root/name.##.ext

extractstreamer_exit(): extract streamer: end an instance. the object should no longer be used after calling this function

extractstreamer_extract_to(): extract streamer: extract to external file

extractstreamer_ls(): extract streamer: list all files in current zip-file

extractstreamer_open(): extract streamer: set which file is open

extractstreamer_read_n_lines(): extract streamer: helper function to read N lines

extractstreamer_read_one_line(): extract streamer: helper function to read one line

extractstreamer_showtext(): extract streamer: get content of file, assumed to be text (or this function crashes)

extractstreamer_start(): extract streamer: create an instance

getBascetDockerImage(): Get and install a Bascet docker image.

getBascetSingularityImage(): Get a Bascet image (singularity or docker). It will be cached in the provided directory to avoid downloading it all the time

get_fastq_R2_from_R1(): Get corresponding R2 file. Assumes that the input file is R1

helper_cancel_job_if_file_exists(): Create a piece of script to exit a job early if file exists

is_bam_paired_alignment(): Figure out if a BAM-file is a paired alignment or not

is_fastq(): Check if a file is a FASTQ file

is_paired_fastq(): Check if a file is a paired FASTQ file

lseq(): logarithmic spaced sequence, from emdbook library

make_output_shard_names(): 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

removeBascetDockerImage(): Remove current Bascet docker image

shellscript_make_bash_array(): Helper function: Create array of values in bash scripts

shellscript_make_commalist(): from a,b to "a,b"

template_BascetFunction(): Function template, where basic parameter documentation can be obtained from