RNA Framework is a modular toolkit designed to handle RNA structure probing and post-transcriptional modifications mapping from high-throughput sequencing data. It supports transcriptome-scale analysis of RNA secondary structure using protocols such as CIRS-seq, SHAPE-seq, Structure-seq, DMS-seq, PARS, SHAPE-MaP, and DMS-MaPseq, as well as mapping of post-transcriptional modifications (Ψ, m1A, m6A, m5C, hm5C, 2'-OMe).

Key features: - Automatic reference transcriptome creation (rf-index) - Read preprocessing, adapter trimming, and mapping (rf-map) - Per-base RT-stop/mutation counting and coverage (rf-count) - Reactivity scoring and whole-transcriptome normalization (rf-norm) - RNA secondary structure prediction with probing data (rf-fold) - RNA-RNA interaction mapping (rf-duplex) - Post-transcriptional modification calling (rf-modcall) - Peak calling for RNA immunoprecipitation data (rf-peakcall)