Man pages for yuabrahamliu/proRate
proRate is an R package to infer gene transcription rates with a novel least sum of squares method.
| addtrack | Add gene coordinate track to a gene's rate inference result... |
| calpauseidx | Calculate Pause indeces for genes from a bam file |
| calrate | Calculate gene elongation rate from a pair of Pro-seq or... |
| getexon | Calculate exon coverages for specific gene regions |
| getgc | Calculate GC content for specific gene regions |
| getkmer | Compare the kmer difference between 2 sets of sequences |
| intercompare | Compare gene elongation rates between 2 different conditions |
| intracompare | Divide genes into different quantile groups according to... |
| makegenelist | Generate a GRanges object of UCSC known genes in specific... |
| mcalpauseidx | Calculate Pause indeces for genes for multiple bam files |
| mcalrate | Calculate gene elongation rate for multiple pairs of Pro-seq... |
| metaplot | Generate metagene plots from a bam file |
| mmetaplot | Generate metagene plots for multiple bam files |
| orgintercompareinput | Organize the results from the function 'mcalrate' to a... |
| plotprocessing | Process the results of the functions 'metaplot' and... |
