Files in lakhanp1/chipmine
Analyze ChIP-seq Data
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/p01_get_sample_information.R
R/p03_QC_ChIPseq_summary.R
R/p03_QC_replicate_correlation.R
R/p03_data_import_functions.R
R/p03_data_preprocess_functions.R
R/p03_distribution_plot_functions.R
R/p03_get_narrowpeak_summit_seq.R
R/p03_signal_fold_change_functions.R
R/p04_best_replicate_peakset.R
R/p04_combinatorial_binding_matrix.R
R/p04_get_TF_binding_data.R
R/p04_peak_target_matrix.R
R/p05_merged_profile_matrix_cluster.R
R/p05_profile_matrix_import_functions.R
R/p05_profile_matrix_kmeans.R
R/p06_gene_length_heatmap_annotation.R
R/p06_profile_heatmap.R
R/p06_profile_plot_list_functions.R
R/p06_signal_heatmap.R
R/p07_annotation_decoration_functions.R
R/p08_average_profile_functions.R
R/p09_coverage_functions.R
R/p99_matrix_scaling_functions.R
R/p99_package_globals.R
R/p99_roxygen_comments.R
R/p99_utils.R
R/p99_utils_txdb.R
README.md
chipmine.Rproj
data/drawing.pdf
data/drawing.svg
man/add_annotation_titles.Rd
man/best_replicate_peakset.Rd
man/bigwig_profile_matrix.Rd
man/chip_summary.Rd
man/combinatorial_binding_matrix.Rd
man/compare_ChIPseq_replicates.Rd
man/compare_replicates.Rd
man/draw_avg_profile_plot.Rd
man/gene_length_heatmap_annotation.Rd
man/geneset_average_profile.Rd
man/get_TES.Rd
man/get_TF_binding_data.Rd
man/get_expression_heatmap_list.Rd
man/get_fold_change.Rd
man/get_peak_summit_seq.Rd
man/get_polII_expressions.Rd
man/get_polII_signal.Rd
man/get_profile_plot_list.Rd
man/get_sample_information.Rd
man/get_txdb_exons_gr.Rd
man/get_txdb_fiveUtr_gr.Rd
man/get_txdb_introns_gr.Rd
man/get_txdb_threeUtr_gr.Rd
man/get_txdb_transcripts_gr.Rd
man/hello.Rd
man/import_peaks_as_df.Rd
man/import_profile_from_file.Rd
man/import_profiles.Rd
man/merged_profile_matrix_cluster.Rd
man/multi_profile_plots.Rd
man/na_impute.Rd
man/peak_target_matrix.Rd
man/plot_MA_gg.Rd
man/plot_scatter.Rd
man/preProcess_polII_expression.Rd
man/profile_heatmap.Rd
man/profile_matrix_kmeans.Rd
man/region_coverage.Rd
man/region_coverage_matrix.Rd
man/scale_matrix_columns.Rd
man/scale_matrix_rows.Rd
man/signal_heatmap.Rd
