Man pages for zslastman/RiboStan
Estimates Isoform Specific RPF Footprint Densities

add_cor_offsetAdd 'correct offset' column to a set of reads
addphaseAdd 'phase' column to a set of reads, given a vector of cds...
chr22_annoGencode v32 annotation for human chromosome 22
convert_gtfConvert old-style gtfs (e.g. those output by rtracklayer) to...
export_codon_dtsCreate a dataframe with a_site, p_site and e site occupancies
fmcolsPick columns from a GRangestList
ftest_orfsRun Multitaper Tests on All ORFs
ftestvectTest a numeric vector for periodicity using the multitaper...
gene_level_elongAggregate transcript elongation scores to gene level
gene_level_exprAggregate transcript level RiboPMs to the gene-level Ignores...
get_cds_codonsGet A Granges object with locations of each codon in the...
get_cdsgrlGet a set of filtered cds from an imported GTF GRanges
get_cds_readsFilter an RPF GR for overlap with coding sequences
get_codon_occsEstimate per codon occupancies
get_codposdfGenerate a data frame of orf_id,position,codon
get_cov_rust_scoresGet A Granges object with locations of each codon in the...
get_exprfileGiven a bam file, and transcript fasta, output a file of...
get_incl_max_offsetsGet Offsets by maximizing p-sites within the CDS
get_kl_dfCalculate KL-divergence from a data frame of rust expected...
get_metacodon_profsGet A Granges object with locations of each codon in the...
get_offsetsGet Offsets by maximizing p-sites within the CDS
get_orf_elongGet the mean dwell time over all translated codons for a set...
get_psitecovGet a coverage RleList of psite coverage over a set of ORFs
get_psite_grconvert a granges object of footprints to a psites object
get_readgrRead and filter a bam file of RPFs
get_readlensSelect those read lengths which make up 95% of the reads
get_read_spmatget_read_spmat
get_ribofasta_annoThis creates a minimal annotation object from a gencode style...
get_ritpmsget_ritpms
get_sitedfcreate a data frame with a and p site codons, and rpf counts...
get_trspace_cdsGet CDS positions in transcript space
hasMstartCheck if a granges list of CDS have start codons
is_out_of_boundsCheck if GRanges elements are out of chromosome bounds
load_annotationGet a set of filtered cds from an imported GTF GRanges
make_ext_fastaCreate a fasta file of coding sequences extended nbp on...
mergeseqlevelsMerge the seqlevels of two Granges objects This function...
metacodondfA data frame containing metacodon data
most_freqGet the most frequent element from a numeric vector
offsets_dfA Dataframe containing CDS-occupancy derived offsets for the...
optimize_ritpmsUse a sparse mapping matrix to optimize ritpms
order_grl_stIndex vector for a GRanges list object with the sub-elements...
periodicity_filter_uORFsRun Multitaper tests on a set of ORFs
pipePipe operator
plot_kl_dvPlot KL divergence in selected windows
read_ribobamRead a bam file containing Ribosomal Footprints
resize_grlResize a GRangesList object, respecting exon boundaries when...
resize_grl_endfixResize a GRangesList object holding it's 3' end fixed
resize_grl_startfixResize a GRangesList object holding it's 5' end fixed
rpfsGRanges object with 63346 ranges and 1 metadata column:
sample_cols_spmatsample_cols_spmat
sample_cov_grsample_cov_gr
select_offsetsGet a dataframe with p-site offsets from a datafram of KL...
sort_grl_stSort a GRanges list object with the sub-elements ordered 5'...
spl_mapFromTranscriptsMap From a transcript to the genome, splitting elements by...
subset_annotationSubset an annotation object with a vector of ORF ids
width1grsgiven a granges object, convert it to width1 granges,...
zslastman/RiboStan documentation built on June 12, 2024, 1:59 a.m.