Files in goodarzilab/Ribolog
Logistic-regression-based analysis of ribosome profiling data
.Rbuildignore
.gitignore
Biomart_cDNA_fasta_to_rW_annotation_and_reheadered_longest_CDS_cDNA_fasta_v2.py
DESCRIPTION
LICENSE
NAMESPACE
R/MODULE_1_CELP_BIAS.R
R/MODULE_2_PREP.R
R/MODULE_3_QC_PCA.R
R/MODULE_4_TER_BASE.R
R/MODULE_5_TER_ALT.R
R/MODULE_6_ORF_CODON.R
R/MODULE_CODON_ANALYSIS.R
README.md
Ribolog.Rproj
Ribolog_Basic_Tutorial.ipynb
benchmarks/Ribolog_benchmark_v3.pdf
data-raw/rpf_corrected_sum_LMCN
data-raw/rr_LMCN
data/arabidopsis_annotation.rda
data/arabidopsis_cdna.rda
data/arabidopsis_id_mapper.rda
data/fly_annotation.rda
data/fly_cdna.rda
data/fly_id_mapper.rda
data/human_annotation.rda
data/human_cdna.rda
data/human_id_mapper.rda
data/maize_annotation.rda
data/maize_cdna.rda
data/maize_id_mapper.rda
data/mouse_annotation.rda
data/mouse_cdna.rda
data/mouse_id_mapper.rda
data/rat_annotation.rda
data/rat_cdna.rda
data/rat_id_mapper.rda
data/worm_annotation.rda
data/worm_cdna.rda
data/worm_id_mapper.rda
data/yeast_annotation.rda
data/yeast_cdna.rda
data/yeast_id_mapper.rda
data/zebrafish_annotation.rda
data/zebrafish_cdna.rda
data/zebrafish_id_mapper.rda
environment.yml
man/CELP_bias.Rd
man/CELP_detect_bias.Rd
man/TER_all_pairs.Rd
man/add_sd_z.Rd
man/adj_TER_p.Rd
man/bam2count.Rd
man/bamtolist_rW.Rd
man/codon2transcript.Rd
man/comb_cor_p.Rd
man/create_te.Rd
man/frame_psite_length_rW.Rd
man/frame_psite_rW.Rd
man/generate_ENZ.Rd
man/generate_correlogram.Rd
man/gm_mean.Rd
man/gm_mean_z.Rd
man/logit_seq.Rd
man/meta_test.Rd
man/metaprofile_psite_rW.Rd
man/min_count_filter.Rd
man/normalize_median_of_ratios.Rd
man/normalize_median_of_ratios_append.Rd
man/pairs2correlograms.Rd
man/pairs2pi0s.Rd
man/partition_to_uniques.Rd
man/pca_qc.Rd
man/plot_mirrors_CELP.Rd
man/print_period_region.Rd
man/print_period_region_length.Rd
man/print_read_end_heatmap.Rd
man/print_read_ldist.Rd
man/print_rop.Rd
man/psite_info_rW.Rd
man/psite_rW.Rd
man/psite_to_codon_count.Rd
man/read_annotation.Rd
man/rends_heat_rW.Rd
man/rlength_distr_rW.Rd
man/row_center.Rd
man/row_standardize.Rd
man/test_ENZ.Rd
man/visualize_CELP.Rd
vignettes/.gitignore
vignettes/Logo3.png
vignettes/RIBOLOG.pdf
vignettes/R_markdown/MODULE1_vignette.Rmd
vignettes/R_markdown/MODULE2_vignette.Rmd
vignettes/R_markdown/MODULE3_vignette.Rmd
vignettes/R_markdown/MODULE4_vignette.Rmd
vignettes/R_markdown/MODULE5_vignette.Rmd
vignettes/Ribolog_workflow.v5.png
