Man pages for coregenomics/groHMM
GRO-seq Analysis Pipeline
| breakTranscriptsOnGenes | breakTranscriptsOnGenes Breaks transcripts on genes |
| combineTranscripts | combineTranscripts Combines transcripts. |
| detectTranscripts | detectTranscripts detects transcripts de novo using a... |
| evaluateHMMInAnnotations | evaluateHMM Evaluates HMM calling. |
| expressedGenes | Function identifies expressed features using the methods... |
| getTxDensity | getTxDensity Calculates transcript density. |
| groHMM-package | groHMM: GRO-seq Analysis Pipeline |
| limitToXkb | limitToXkb truncates a set of genomic intervals at a... |
| makeConsensusAnnotations | makeConsensusAnnotations Makes a consensus annotation |
| metaGene | Returns a histogram of the number of reads in each section of... |
| pausingIndex | Returns the pausing index for different genes. TODO:... |
| polymeraseWave | Given GRO-seq data, identifies the location of the polymerase... |
| RgammaMLE | RgammaMLE fits a gamma distribution to a specified data... |
| Rnorm | Rnorm fits a normal distribution to a specified data vector... |
| Rnorm.exp | Rnorm.exp fits a normal+exponential distribution to a... |
| runMetaGene | Runs meta gene analysis for sense and anti-sense direction. |
| windowAnalysis | windowAnalysis Returns a vector of integers representing the... |
