Files in ohlerlab/RiboseQC
RiboseQC, a Comprehensive Ribo-Seq Analysis Tool
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/FaFile_Circ.R
R/riboseq_analysis.R
R/riboseqc.R
README.md
RiboseQC-manual.pdf
RiboseQC.R
RiboseQC.Rmd
RiboseQC.Rproj
RiboseQC.html.REMOVED.git-id
TODOS.R
ex/cds_txs_coords_similbed.bed
ex/fiveutrs_similbed.bed
ex/genetic_codes
ex/introns_similbed.bed
ex/ncIsof_similbed.bed
ex/ncRNAs_similbed.bed
ex/root_P_sites_minus.bedgraph
ex/root_P_sites_plus.bedgraph
ex/root_P_sites_uniq_minus.bedgraph
ex/root_P_sites_uniq_plus.bedgraph
ex/root_coverage_minus.bedgraph
ex/root_coverage_plus.bedgraph
ex/root_coverage_uniq_minus.bedgraph
ex/root_coverage_uniq_plus.bedgraph
ex/root_junctions
ex/seqinfo
ex/simp_arab.fa.gz
ex/simp_arab.fa.gz.fai
ex/simp_arab.gtf.gz_Rannot
ex/simp_arab.gtf.gz_TxDb
ex/table_gene_tx_IDs
ex/threeutrs_similbed.bed
ex/tmp_RiboseQC_root/P_sites_stats
ex/tmp_RiboseQC_root/profiles_P_sites
ex/tmp_RiboseQC_root/profiles_fivepr
ex/tmp_RiboseQC_root/read_stats
ex/tmp_RiboseQC_root/selection_cutoffs
inst/NEWS
inst/ext_data/root_results_RiboseQC
inst/ext_data/shoots_results_RiboseQC
inst/ext_data/simp_arab.fa.gz
inst/ext_data/simp_arab.gtf.gz
inst/ext_data/simp_arab_root.bam
inst/ext_data/simp_arab_root.bam.bai
inst/ext_data/simp_arab_shoots.bam
inst/ext_data/simp_arab_shoots.bam.bai
inst/rmd/riboseqc_template.Rmd
inst/rmd/riboseqc_template_full.Rmd
inst/script/creating_test_data.R
man/FaFile_Circ-class.Rd
man/RiboseQC_analysis.Rd
man/calc_cutoffs_from_profiles.Rd
man/choose_readlengths.Rd
man/create_html_report.Rd
man/create_pdfs_from_rds_objects.Rd
man/generate_rdata_list.Rd
man/getSeq-FaFile_Circ-method.Rd
man/get_codon_usage_data.Rd
man/get_default_rl_selection.Rd
man/get_metagene_data.Rd
man/get_ps_fromsplicemin.Rd
man/get_ps_fromspliceplus.Rd
man/get_rl_and_cutoffs.Rd
man/get_top50_all_genes.Rd
man/get_top50_cds_genes.Rd
man/get_top50_mapping.Rd
man/load_annotation.Rd
man/plot_codon_usage_bulk.Rd
man/plot_codon_usage_bulk_rmd.Rd
man/plot_codon_usage_positional.Rd
man/plot_codon_usage_positional_rmd.Rd
man/plot_frame_dist_boxplot.Rd
man/plot_frame_dist_boxplot_rmd.Rd
man/plot_metagene_bar.Rd
man/plot_metagene_bar_rmd.Rd
man/plot_metagene_hm.Rd
man/plot_metagene_hm_rmd.Rd
man/plot_read_biotype_dist_1.Rd
man/plot_read_biotype_dist_2.Rd
man/plot_read_biotype_dist_by_length.Rd
man/plot_read_length_dist.Rd
man/plot_read_length_dist_by_biotype.Rd
man/prepare_annotation_files.Rd
man/seqinfo-FaFile_Circ-method.Rd
tests/testthat.R
tests/testthat/test_FaFile_Circ.R
tests/testthat/test_cuttoff_sel.R
tests/testthat/test_main.R
vignettes/.build.timestamp
vignettes/RiboseQC.R
