Files in cparsania/parcutils
Utility Functions To Deal Day To Day Bioinformatics Tasks.

.DS_Store
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.Rprofile
.github/.gitignore
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/chip_related.R R/general_bioinfo.R R/internal.R R/ir_realted.R R/rnaseq_related.R R/s3_methods.R R/splicewiz_wrappers.R R/viz_related.R README.Rmd README.md
_pkgdown.yml
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js
docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.1.0/bootstrap.min.css
docs/deps/data-deps.txt
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/EnhancedVolcano2.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/Rplot003.png
docs/reference/Rplot004.png
docs/reference/Rplot005.png
docs/reference/Rplot006.png
docs/reference/Rplot007.png
docs/reference/annotate_retained_introns.html
docs/reference/categorize_diff_genes.html
docs/reference/dot-assign_class_irFinderSdata.html
docs/reference/dot-assign_intron_identifier.html
docs/reference/dot-categorize_diff_ase.html
docs/reference/dot-categorize_diff_genes.html
docs/reference/dot-check_mendate_columns_for_irFinderSdata.html
docs/reference/dot-count_data_convert_NA_to_0.html
docs/reference/dot-dsr_to_tibble.html
docs/reference/dot-filter_df_by_genes.html
docs/reference/dot-filter_gff.html
docs/reference/dot-filter_orgdb_by_genetype.html
docs/reference/dot-filter_rows_from_count_data.html
docs/reference/dot-fix_ASE_diff_rslt_columns.html
docs/reference/dot-fix_hm_colors.html
docs/reference/dot-fix_splicewiz_res_edger_columns.html
docs/reference/dot-generate_a_lineplot.html
docs/reference/dot-generate_go_emap_plot.html
docs/reference/dot-get_aes_heatmap_data.html
docs/reference/dot-get_all_expressed_genes.html
docs/reference/dot-get_all_named_expression_matrix.html
docs/reference/dot-get_ase_heatmap_data.html
docs/reference/dot-get_count_data.html
docs/reference/dot-get_gene_groups_for_fc_scatter_plot.html
docs/reference/dot-get_intron_annotations.html
docs/reference/dot-get_parcutils_obj_gene_names.html
docs/reference/dot-get_parcutils_object_example.html
docs/reference/dot-get_sample_information.html
docs/reference/dot-group_replicates_by_sample.html
docs/reference/dot-is_genes_present_in_obj_parcutils.html
docs/reference/dot-is_sample_comparsions_present_in_obj_parcutils.html
docs/reference/dot-keep_only_enriched_go.html
docs/reference/dot-map_granges_metadata.html
docs/reference/dot-mark_ir_status_by_filters.html
docs/reference/dot-parallel_import_bw_files.html
docs/reference/dot-parcutils_assign_intron_identifier.html
docs/reference/dot-perform_kemans_cluster.html
docs/reference/dot-piarwise_upset.html
docs/reference/dot-prepare_parcutils_ir.html
docs/reference/dot-save_de_ir_results.html
docs/reference/dot-save_deg_results.html
docs/reference/dot-simplify_go.html
docs/reference/dot-validate_a_list_of_normalised_matrix.html
docs/reference/dot-validate_irfinders_object.html
docs/reference/dot-validate_parcutils_chip.html
docs/reference/dot-validate_parcutils_ir_object.html
docs/reference/dot-validate_parcutils_obj.html
docs/reference/dsr_to_tibble.html
docs/reference/enrichMsigDB.html
docs/reference/event_region_to_coordinate.html
docs/reference/event_region_to_granges.html
docs/reference/figures/README-fig.width==4-1.png
docs/reference/figures/README-fig.width==4-2.png
docs/reference/figures/README-pressure-1.png
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docs/reference/filter_gff.html
docs/reference/fix_hm_colors.html
docs/reference/get_ASE_by_regulation.html
docs/reference/get_ASE_counts_barplot-1.png
docs/reference/get_ASE_counts_barplot.html
docs/reference/get_ASE_data_matrix.html
docs/reference/get_all_named_expression_matrix.html
docs/reference/get_ase_data_matrix_heatmap-1.png
docs/reference/get_ase_data_matrix_heatmap-2.png
docs/reference/get_ase_data_matrix_heatmap-3.png
docs/reference/get_ase_data_matrix_heatmap.html
docs/reference/get_ase_volcano_plot-1.png
docs/reference/get_ase_volcano_plot-2.png
docs/reference/get_ase_volcano_plot-3.png
docs/reference/get_ase_volcano_plot.html
docs/reference/get_chip_signal_heatmap.html
docs/reference/get_chip_signal_over_control_heatmap.html
docs/reference/get_corr_heatbox-1.png
docs/reference/get_corr_heatbox.html
docs/reference/get_deg.html
docs/reference/get_diff_ASE_count_barplot-1.png
docs/reference/get_diff_ASE_count_barplot.html
docs/reference/get_diff_ase_heatmap-1.png
docs/reference/get_diff_ase_heatmap-2.png
docs/reference/get_diff_ase_heatmap.html
docs/reference/get_diff_gene_count_barplot-1.png
docs/reference/get_diff_gene_count_barplot.html
docs/reference/get_edger_diff_ase_event_names.html
docs/reference/get_event_annotations.html
docs/reference/get_five_prime_flank_motif.html
docs/reference/get_fold_change_matrix.html
docs/reference/get_fold_change_scatter_plot-1.png
docs/reference/get_fold_change_scatter_plot-2.png
docs/reference/get_fold_change_scatter_plot-3.png
docs/reference/get_fold_change_scatter_plot.html
docs/reference/get_gene_expression_box_plot-1.png
docs/reference/get_gene_expression_box_plot-2.png
docs/reference/get_gene_expression_box_plot.html
docs/reference/get_gene_expression_heatmap-1.png
docs/reference/get_gene_expression_heatmap-2.png
docs/reference/get_gene_expression_heatmap-3.png
docs/reference/get_gene_expression_heatmap-4.png
docs/reference/get_gene_expression_heatmap-5.png
docs/reference/get_gene_expression_heatmap-6.png
docs/reference/get_gene_expression_heatmap-7.png
docs/reference/get_gene_expression_heatmap.html
docs/reference/get_gene_expression_line_plot-1.png
docs/reference/get_gene_expression_line_plot-2.png
docs/reference/get_gene_expression_line_plot-3.png
docs/reference/get_gene_expression_line_plot-4.png
docs/reference/get_gene_expression_line_plot-5.png
docs/reference/get_gene_expression_line_plot.html
docs/reference/get_genes_by_regulation.html
docs/reference/get_genes_from_event_name.html
docs/reference/get_go_emap_plot-1.png
docs/reference/get_go_emap_plot.html
docs/reference/get_heatmap_data.html
docs/reference/get_intergenic_signals.html
docs/reference/get_intron_master_list.html
docs/reference/get_ir_counts.html
docs/reference/get_normalised_expression_matrix.html
docs/reference/get_pairwise_corr_plot-1.png
docs/reference/get_pairwise_corr_plot-2.png
docs/reference/get_pairwise_corr_plot-3.png
docs/reference/get_pairwise_corr_plot.html
docs/reference/get_pca_plot-1.png
docs/reference/get_pca_plot-2.png
docs/reference/get_pca_plot-3.png
docs/reference/get_pca_plot.html
docs/reference/get_replicates_by_sample.html
docs/reference/get_rpkm.html
docs/reference/get_splicewiz_ase_heatmap-1.png
docs/reference/get_splicewiz_ase_heatmap-2.png
docs/reference/get_splicewiz_ase_heatmap.html
docs/reference/get_splicewiz_event_counts-1.png
docs/reference/get_splicewiz_event_counts.html
docs/reference/get_star_align_log_summary.html
docs/reference/get_star_align_log_summary_plot-1.png
docs/reference/get_star_align_log_summary_plot-2.png
docs/reference/get_star_align_log_summary_plot.html
docs/reference/get_star_aling_log_summary.html
docs/reference/get_thee_prime_flank_motif.html
docs/reference/get_three_prime_flank_motif.html
docs/reference/get_tpm.html
docs/reference/get_upset_intersects.html
docs/reference/get_volcano_plot-1.png
docs/reference/get_volcano_plot-2.png
docs/reference/get_volcano_plot-3.png
docs/reference/get_volcano_plot.html
docs/reference/ggsave2.html
docs/reference/group_replicates_by_sample.html
docs/reference/gseMsigDB.html
docs/reference/gsea_analysis.html
docs/reference/gsea_msigdb.html
docs/reference/import_topn_bed_features.html
docs/reference/index.html
docs/reference/make_enriched_heatmap_list.html
docs/reference/make_parcutils_chip.html
docs/reference/map_intron_meta_data.html
docs/reference/mark_ir_status_by_filters.html
docs/reference/named_group_split.html
docs/reference/normalise_counts.html
docs/reference/normalised_matrix_to_rpm.html
docs/reference/parcutils_chip-class.html
docs/reference/parcutils_get_introns.html
docs/reference/piarwise_upset.html
docs/reference/plot_chip_pairwise_correlation_heatmap.html
docs/reference/plot_deASE_venn-1.png
docs/reference/plot_deASE_venn-2.png
docs/reference/plot_deASE_venn-3.png
docs/reference/plot_deASE_venn.html
docs/reference/plot_deg_upsets-1.png
docs/reference/plot_deg_upsets.html
docs/reference/plot_deg_venn-1.png
docs/reference/plot_deg_venn-2.png
docs/reference/plot_deg_venn-3.png
docs/reference/plot_deg_venn.html
docs/reference/plot_regions_relative_to_reference.html
docs/reference/print.html
docs/reference/print.parcutils.html
docs/reference/print.parcutils_ase.html
docs/reference/print.parcutils_ir.html
docs/reference/read_irfinderS_output.html
docs/reference/run_ase_diff_analysis.html
docs/reference/run_deseq_analysis.html
docs/reference/run_deseq_analysis_ir.html
docs/reference/save_de_results.html
docs/reference/save_go_data.html
docs/reference/save_go_plots.html
docs/reference/save_go_results.html
docs/reference/select_cols_irfinderS_output.html
docs/reference/sort_geom_box-1.png
docs/reference/sort_geom_box-2.png
docs/reference/sort_geom_box-3.png
docs/reference/sort_geom_box-4.png
docs/reference/sort_geom_box.html
docs/reference/spliceWiz_plot_event_counts.html
docs/reference/validata_parcutils_obj.html
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inst/extdata/.DS_Store
inst/extdata/Homo_sapiens.GRCh38.101.gtf.gz
inst/extdata/a_Log.final.out
inst/extdata/b_Log.final.out
inst/extdata/c_Log.final.out
inst/extdata/d_Log.final.out
inst/extdata/e_Log.final.out
inst/extdata/example.bw
inst/extdata/f_Log.final.out
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inst/extdata/instruct.txt
inst/extdata/ir_data/.DS_Store
inst/extdata/ir_data/ctrl_rep1-IR-nondir.txt
inst/extdata/ir_data/ctrl_rep2-IR-nondir.txt
inst/extdata/ir_data/treat_rep1-IR-nondir.txt
inst/extdata/ir_data/treat_rep2-IR-nondir.txt
inst/extdata/sample_information
inst/extdata/toy_counts.txt
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parcutils.Rproj
renv.lock
renv/.gitignore
renv/activate.R
renv/settings.dcf
cparsania/parcutils documentation built on Oct. 27, 2024, 4:55 a.m.