Man pages for ohlerlab/RiboseQC
Ribo-seQC, a comprehensive Ribo-seq analysis tool

calc_cutoffs_from_profilesCalculate offsets from 5'end profiles
choose_readlengthsFilter read lengths for P-sites position calculation
create_html_reportCreate the Ribo-seQC analysis report in html
create_pdfs_from_rds_objectsGenerate PDF files from RDS object files
generate_rdata_listGenerate a list of R data objects
get_codon_usage_dataGet codon usage data (positional and bulk)
get_default_rl_selectionGet default choice of read lengths
get_metagene_dataGet 5'/P-site profile data for metagene analysis
get_ps_fromspliceminOffset spliced reads on minus strand
get_ps_fromspliceplusOffset spliced reads on plus strand
get_rl_and_cutoffsGet selected read lengths and cutoffs
get_top50_all_genesGet top 50 abundant genes (all genes)
get_top50_cds_genesGet top 50 abundant genes (CDS regions for protein coding...
get_top50_mappingGet top 50 mapping positions
load_annotationLoad genomic features and genome sequence
plot_codon_usage_bulkPlot bulk codon usage bar plots
plot_codon_usage_bulk_rmdPlot bulk codon usage bar plots within the RMarkdown document
plot_codon_usage_positionalPlot positional codon usage heatmap
plot_codon_usage_positional_rmdPlot positional codon usage heatmaps within the RMarkdown...
plot_frame_dist_boxplotPlot frame coverage of 5'-site profiles
plot_frame_dist_boxplot_rmdPlot frame coverage of 5'-site profiles within the RMarkdown...
plot_metagene_barPlot 5'/P-site profile per read length as barplot
plot_metagene_bar_rmdPlot 5'/P-site profile per read length as barplot in R...
plot_metagene_hmPlot 5'/P-site profiles (for all read lengths) as heatmap
plot_metagene_hm_rmdPlot 5'/P-site profiles as heatmaps within the RMarkdown...
plot_read_biotype_dist_1Plot read location distribution by biotype (and originating...
plot_read_biotype_dist_2Plot read location distribution by originating compartment...
plot_read_biotype_dist_by_lengthPlot read length and location distribution (distribution per...
plot_read_length_distPlot read length distribution
plot_read_length_dist_by_biotypePlot read length and location distribution (distribution per...
prepare_annotation_filesPrepare comprehensive sets of annotated genomic features
RiboseQC_analysisPerform a Ribo-seQC analysis
ohlerlab/RiboseQC documentation built on March 23, 2019, 12:11 a.m.