Man pages for anthony-aylward/exploreatacseq
Exploratory Analysis of ATAC-seq data
| consensus_peaks | Consensus peaks |
| coordinates_by_treatment | coordinates by treatment |
| count_dgelist | DGEList of read counts |
| explore | Explore ATAC-seq data |
| exploreatacseq_color_palette | tailored color palette |
| extract_batch_vector | extract batch |
| extract_group_vector | extract group |
| extract_peaks_paths_by_sample | extract peaks paths by sample |
| extract_reads_file_paths | extract reads file paths |
| extract_sample_vector | extract sample vector |
| extract_treatment_vector | extract treatment vector |
| extract_tss_enrichments | extract TSS enrichments |
| filter_peaks | Filter peaks |
| generate_pca_plots | generate PCA plots |
| get_raw_counts | Matrix of raw read counts |
| locate_SCATEData_files | locate SCATEData files |
| map_paths_to_samples | map SCATEData file paths to sample types |
| median_peak_length | Median Peak Length |
| most_variable_peaks | most variable peaks |
| parse_input_data | parse input data |
| parse_json | parse input JSON |
| peaks_by_sample | Peaks by sample |
| plot_pca | plot principal components |
| preprocess | preprocess ATAC-seq data |
| read_peaks | Read peaks from a file |
| SCATEData_accession_sample | Table mapping SCATEData accession numbers to sample type |
| SCATEData_sample | Vector mapping SCATEData accession numbers to sample type |
| transform_counts | apply transformations to read counts |
| unify_granges | Unify GRanges |
| unify_peaks | Unify peaks |
