Reference

Main Functions Primary user-facing functions
mpaqt_index()	Create MPAQT Index
mpaqt_prepare_short_reads()	Prepare Short-Read Data for Quantification
mpaqt_prepare_short_reads_sc()	Prepare Single-Cell Short-Read Data
mpaqt_prepare_long_reads()	Prepare Long-Read Data for Quantification
mpaqt_prepare_long_reads_sc()	Prepare Single-Cell Long-Read Data
mpaqt_prepare_long_reads_sc_flnc()	Prepare Single-Cell Long-Read Data from FLNC FASTQ
mpaqt_quant()	Quantify Transcript Abundances
mpaqt_quant_bulk()	Quantify Transcript Abundances (Bulk RNA-seq)
mpaqt_quant_sc()	Quantify Transcript Abundances (Single-Cell RNA-seq)
mpaqt_prequant()	Run Pre-Quantification Phase
mpaqt_postquant()	Run Post-Quantification Phase
Results Working with quantification results
tpm()	Extract TPM values from quantification result
abundances()	Extract raw abundances from quantification result
gene_abundances()	Aggregate transcript abundances to gene level
uncertainty()	Extract Uncertainty Estimates
has_uncertainty()	Check if Result Has Uncertainty Estimates
export_results_csv()	Export results to CSV
export_combined_results()	Export Combined Results to CSV
combine_quant_results()	Combine Multiple Quantification Results
get_parameters()	Get Algorithm Parameters
get_input_metadata()	Get Input Metadata
I/O Functions Reading and writing data
mpaqt_read_index()	Load MPAQT Index from Disk
mpaqt_read_counts()	Load counts from disk
mpaqt_read_result()	Load quantification result from disk
mpaqt_read_short_read_counts()	Load Pre-Processed Short-Read Counts
mpaqt_read_long_read_counts()	Load Pre-Processed Long-Read Counts
mpaqt_read_prequant()	Load pre-quantification result
mpaqt_save_result()	Save Quantification Results
mpaqt_save_result_sc()	Save Single-Cell Quantification Results
mpaqt_save_prequant()	Save pre-quantification result
Processing Functions Low-level read processing
mpaqt_process_short_reads()	Process Short-Read FASTQ Files (Bulk)
mpaqt_process_short_reads_sc()	Process Short-Read FASTQ Files (Single-Cell)
mpaqt_process_long_reads()	Process Long-Read Count File (Bulk)
mpaqt_process_long_reads_sc()	Process Long-Read Count File (Single-Cell)
Dependency Checks Check for optional dependencies
require_long_read_processing()	Check Requirements for Long-Read Processing
require_sc_long_read_flnc()	Check Requirements for Single-Cell Long-Read FLNC Processing
require_transcriptome_extraction()	Check Requirements for Transcriptome Extraction from GTF
S3 Methods Print, summary, and accessor methods
coef(<mpaqt_quant_result>)	Extract coefficients (abundances) from quantification result
fitted(<mpaqt_quant_result>)	Extract fitted values from quantification result
print(<mpaqt_counts_lr>)	Print method for mpaqt_counts_lr
print(<mpaqt_counts_sr>)	Print method for mpaqt_counts_sr
print(<mpaqt_index>)	Print method for mpaqt_index
print(<mpaqt_prequant>)	Print method for mpaqt_prequant
print(<mpaqt_quant_result>)	Print method for mpaqt_quant_result
summary(<mpaqt_counts_lr>)	Summary method for mpaqt_counts_lr
summary(<mpaqt_counts_sr>)	Summary method for mpaqt_counts_sr
summary(<mpaqt_index>)	Summary method for mpaqt_index
summary(<mpaqt_quant_result>)	Summary method for mpaqt_quant_result
length(<mpaqt_counts>)	Get number of elements in counts object
length(<mpaqt_index>)	Get number of transcripts in index
`[`(<mpaqt_counts>)	Extract counts vector
`[`(<mpaqt_index>)	Subset an mpaqt_index by transcript indices