Man pages for SamBuckberry/RunATAC
Functions for Importing, Processing, Analyzing, Plotting and Reformatting ATAC-seq Data
| bam_to_centres_bw | Write a bigwig file of Tn5 insertion depth |
| bam_to_insertions_bw | Write a bigwig file of Tn5 insertion depth |
| calc_dinuc_freq | Calculate the dinucleotide insertion frequency for Tn5... |
| calc_frip | Calculate the fraction of reads in peaks. |
| calc_ins_bias | Calculate the PWM for Tn5 insertions. |
| calc_ins_pwm | Calculate the PWM for Tn5 insertions. |
| calc_motif_dist | Calculate distances of Tn5 insertions from motif. |
| calc_v | Calculate distances of Tn5 insertions from motif. |
| motif_gr | Get the positions of the PWM in ATAC-seq peaks. |
| plot_insert_size | Plot insert size historgram |
| plot_scaled_footprint | Plot scaled ATAC-seq footprint signal. |
| plot_v | Calculate distances of Tn5 insertions from motif. |
| range_summary | Get the signal from bigwig file for defined regions. |
| read_atac_frags | Read BAM file aligned fragments into GRanges object |
| read_atac_insertions | Read BAM file Tn5 insertion positions into GRanges object |
| read_bed | Read BED formatted file to GRanges object |
| write_gr_bed | Write ranges in a GenomicRanges object to a BED file |
| write_insertions_bw | Write a bigwig file of Tn5 insertion depth |
| write_nuc_bw | Write bigwig file of nucleosome depth |
