Man pages for luisvalesilva/hwglabr
Collection of R functions used in the Hochwagen Lab
| chr_coverage | Average signal per chromosome |
| chr_coverage_plot | Average chromosome signal (coverage) dot plot |
| facs_density_plot | FACS density plot |
| FE2 | Microarray probe log2 ratios |
| genome_average | Calculate genome-wide average signal |
| gff_get_attribute | Parse gff field |
| gff_read | Read gff file |
| hwglabr | hwglabr: A compilation of functions used frequently by... |
| opening_act | Standard analysis of ChIP-seq experiments |
| opening_act_batch_run | Batch run of 'opening_act' function |
| order_chromosomes | Order chromosome column by chromosome length |
| plot_gene_arrow | Plot genes on an R wiggle plot |
| readall_tab | Load wiggle data |
| remove_centromeres | Remove centromeric regions from wiggle data |
| rna_seq_analysis | Wrapper function to run edgeR analysis of summarized reads... |
| signal_at_conv | Signal between all convergent genes genome-wide |
| signal_at_conv_average_plot | Line plot of average signal between convergent genes |
| signal_at_intergen | Signal at intergenic regions between convergent, divergent or... |
| signal_at_intergen_average_plot | Line plot of average signal on intergenic regions |
| signal_at_orf | Signal at all ORFs genome-wide (meta ORF) |
| signal_at_orf_average_plot | Line plot of average signal on ORFs |
| signal_at_orf_se | Signal around ORF start or end positions |
| signal_at_rDNA | Signal flanking rDNA |
| signal_at_summit | Signal around all bedfile midpoints |
| signal_average | Calculate average signal by position |
| signal_from_telomeres | Collect signal from telomeres for all chromosome arms |
| signal_from_telomeres_average | Compute mean signal and SD by position of output of... |
| signal_per_orf_length | Mean signal for all ORFs genome-wide |
| wiggle_compress | Compress wiggle data |
| wiggle_correlation | Correlation between two ChIP-seq experiments |
| wiggle_plot | Wiggle data line plot |
| wiggle_scatter | To make a scatter plot comparison of two wiggle files |
| wiggle_scatter_plot | To make a scatter plot comparison of two wiggle files |
| wiggle_signal_average | Calculate genome-wide signal average in wiggle data |
| wiggle_smooth | Sliding window smooth of wiggle data |
