Man pages for groHMM
GRO-seq Analysis Pipeline
| averagePlot | Returns the average profile of tiling array probe intensity... |
| breakTranscriptsOnGenes | breakTranscriptsOnGenes Breaks transcripts on genes |
| combineTranscripts | combineTranscripts Combines transnscipts. |
| countMappableReadsInInterval | countMappableReadsInInterval counts the number of mappable... |
| detectTranscripts | detectTranscripts detects transcripts de novo using a... |
| evaluateHMMInAnnotations | evaluateHMM Evaluates HMM calling. |
| expressedGenes | Function identifies expressed features using the methods... |
| getCores | Returns the number of cores. |
| getTxDensity | getTxDensity Calculates transcript density. |
| groHMM-package | groHMM: GRO-seq Analysis Pipeline |
| limitToXkb | limitToXkb truncates a set of genomic itnervals at a... |
| makeConsensusAnnotations | makeConsensusAnnotations Makes a consensus annotation |
| metaGene | Returns a histogram of the number of reads in each section of... |
| metaGeneMatrix | Returns a matrix, with rows representing read counts across a... |
| metaGene_nL | 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... |
| readBed | readBed Returns a GenomicRanges object constrcuted from the... |
| 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 metagene analysis for sense and antisense direction. |
| tlsDeming | A 'total least squares' implementation using demming... |
| tlsLoess | A 'total least squares'-like hack for LOESS. Works by... |
| tlsSvd | A 'total least squares' implementation using singular value... |
| windowAnalysis | windowAnalysis Returns a vector of integers representing the... |
| writeWiggle | writeWiggle writes a wiggle track or BigWig file suitable for... |
