| add_cor_offset | Add 'correct offset' column to a set of reads |
| addphase | Add 'phase' column to a set of reads, given a vector of cds... |
| chr22_anno | Gencode v32 annotation for human chromosome 22 |
| convert_gtf | Convert old-style gtfs (e.g. those output by rtracklayer) to... |
| export_codon_dts | Create a dataframe with a_site, p_site and e site occupancies |
| fmcols | Pick columns from a GRangestList |
| ftest_orfs | Run Multitaper Tests on All ORFs |
| ftestvect | Test a numeric vector for periodicity using the multitaper... |
| gene_level_elong | Aggregate transcript elongation scores to gene level |
| gene_level_expr | Aggregate transcript level RiboPMs to the gene-level Ignores... |
| get_cds_codons | Get A Granges object with locations of each codon in the... |
| get_cdsgrl | Get a set of filtered cds from an imported GTF GRanges |
| get_cds_reads | Filter an RPF GR for overlap with coding sequences |
| get_codon_occs | Estimate per codon occupancies |
| get_codposdf | Generate a data frame of orf_id,position,codon |
| get_cov_rust_scores | Get A Granges object with locations of each codon in the... |
| get_exprfile | Given a bam file, and transcript fasta, output a file of... |
| get_incl_max_offsets | Get Offsets by maximizing p-sites within the CDS |
| get_kl_df | Calculate KL-divergence from a data frame of rust expected... |
| get_metacodon_profs | Get A Granges object with locations of each codon in the... |
| get_offsets | Get Offsets by maximizing p-sites within the CDS |
| get_orf_elong | Get the mean dwell time over all translated codons for a set... |
| get_psitecov | Get a coverage RleList of psite coverage over a set of ORFs |
| get_psite_gr | convert a granges object of footprints to a psites object |
| get_readgr | Read and filter a bam file of RPFs |
| get_readlens | Select those read lengths which make up 95% of the reads |
| get_read_spmat | get_read_spmat |
| get_ribofasta_anno | This creates a minimal annotation object from a gencode style... |
| get_ritpms | get_ritpms |
| get_sitedf | create a data frame with a and p site codons, and rpf counts... |
| get_trspace_cds | Get CDS positions in transcript space |
| hasMstart | Check if a granges list of CDS have start codons |
| is_out_of_bounds | Check if GRanges elements are out of chromosome bounds |
| load_annotation | Get a set of filtered cds from an imported GTF GRanges |
| make_ext_fasta | Create a fasta file of coding sequences extended nbp on... |
| mergeseqlevels | Merge the seqlevels of two Granges objects This function... |
| metacodondf | A data frame containing metacodon data |
| most_freq | Get the most frequent element from a numeric vector |
| offsets_df | A Dataframe containing CDS-occupancy derived offsets for the... |
| optimize_ritpms | Use a sparse mapping matrix to optimize ritpms |
| order_grl_st | Index vector for a GRanges list object with the sub-elements... |
| periodicity_filter_uORFs | Run Multitaper tests on a set of ORFs |
| pipe | Pipe operator |
| plot_kl_dv | Plot KL divergence in selected windows |
| read_ribobam | Read a bam file containing Ribosomal Footprints |
| resize_grl | Resize a GRangesList object, respecting exon boundaries when... |
| resize_grl_endfix | Resize a GRangesList object holding it's 3' end fixed |
| resize_grl_startfix | Resize a GRangesList object holding it's 5' end fixed |
| rpfs | GRanges object with 63346 ranges and 1 metadata column: |
| sample_cols_spmat | sample_cols_spmat |
| sample_cov_gr | sample_cov_gr |
| select_offsets | Get a dataframe with p-site offsets from a datafram of KL... |
| sort_grl_st | Sort a GRanges list object with the sub-elements ordered 5'... |
| spl_mapFromTranscripts | Map From a transcript to the genome, splitting elements by... |
| subset_annotation | Subset an annotation object with a vector of ORF ids |
| width1grs | given a granges object, convert it to width1 granges,... |
