Tool	Description
rf-index	Automatically queries UCSC genome database and builds the transcriptome Bowtie reference index for the RF Map module
rf-map	Performs reads pre-processing and mapping
rf-count	Calculates per-base RT-stops/mutations and coverage from transcriptome-level SAM/BAM files, and generates mutation map files for processing with DRACO
rf-count-genome	Calculates per-base RT-stops/mutations and coverage from genome-level SAM/BAM files
rf-normfactor	Calculates experiment-wide normalization factors for use with rf-norm
rf-norm	Performs whole-transcriptome normalization of structure probing data
rf-fold	Produces secondary structures for the analyzed transcripts using structure probing data to guide folding
rf-structextract	Extracts substructures based on certain criteria (e.g. median SHAPE reactivity, median Shannon entropy, stability higher than expected by chance, etc.)
rf-duplex	Analyzes direct RNA-RNA interaction mapping experiments (i.e. COMRADES, SPASH, PARIS, etc.)
rf-compare	Compares secondary structures inferred by rf-fold with a set of reference structures, and computes PPV and sensitivity
rf-eval	Evaluates the agreement between reactivity data and a secondary structure model
rf-jackknife	Iteratively optimize slope and intercept parameters to maximize PPV and sensitivity using a set of reference structures
rf-modcall	Performs analysis of Ψ-seq/Pseudo-seq and 2OMe-seq data
rf-peakcall	Performs peak calling of RNA immunoprecipitation (RIP) experiments
rf-motifdiscovery	Discovers significantly enriched sequence motifs in RIP peaks
rf-combine	Combines results of multiple experiments into a single profile
rf-correlate	Calculates pairwise correlation of structure probing experiments
rf-wiggle	Produces WIGGLE track files from RC or XML input files
rf-rctools	anipulation of RC files
rf-mmtools	Manipulation of MM files
rf-mutate	Designs structure disrupting (and compensatory) mutations
rf-json2rc	Post-processes DRACO JSON output files into RC files