| groHMM-package | groHMM: GRO-seq Analysis Pipeline |
| averagePlot | Returns the average profile of tiling array probe intensity values or wiggle-like count data centered on a set of genomic positions (specified by 'Peaks'). |
| breakTranscriptsOnGenes | breakTranscriptsOnGenes Breaks transcripts on genes |
| combineTranscripts | combineTranscripts Combines transnscipts. |
| countMappableReadsInInterval | countMappableReadsInInterval counts the number of mappable reads in a set of genomic features. |
| detectTranscripts | detectTranscripts detects transcripts de novo using a two-state hidden Markov model (HMM). |
| evaluateHMMInAnnotations | evaluateHMM Evaluates HMM calling. |
| expressedGenes | Function identifies expressed features using the methods introduced in Core, Waterfall, Lis; Science, Dec. 2008. |
| getCores | Returns the number of cores. |
| getTxDensity | getTxDensity Calculates transcript density. |
| groHMM | groHMM: GRO-seq Analysis Pipeline |
| limitToXkb | limitToXkb truncates a set of genomic itnervals at a constant, maximum size. |
| makeConsensusAnnotations | makeConsensusAnnotations Makes a consensus annotation |
| metaGene | Returns a histogram of the number of reads in each section of a moving window centered on a certain feature. |
| metaGeneMatrix | Returns a matrix, with rows representing read counts across a specified gene, or other features of interest. |
| metaGene_nL | Returns a histogram of the number of reads in each section of a moving window of #' variable size across genes. |
| pausingIndex | Returns the pausing index for different genes. TODO: DESCRIBE THE PAUSING INDEX. |
| polymeraseWave | Given GRO-seq data, identifies the location of the polymerase 'wave' in up- or down- regulated genes. |
| readBed | readBed Returns a GenomicRanges object constrcuted from the specified bed file. |
| RgammaMLE | RgammaMLE fits a gamma distribution to a specified data vector using maximum likelihood. |
| Rnorm | Rnorm fits a normal distribution to a specified data vector using maximum likelihood. |
| Rnorm.exp | Rnorm.exp fits a normal+exponential distribution to a specified data vector using maximum likelihood. |
| runMetaGene | Runs metagene analysis for sense and antisense direction. |
| tlsDeming | A 'total least squares' implementation using demming regression. |
| tlsLoess | A 'total least squares'-like hack for LOESS. Works by rotating points 45 degrees, fitting LOESS, and rotating back. |
| tlsSvd | A 'total least squares' implementation using singular value demposition. |
| windowAnalysis | windowAnalysis Returns a vector of integers representing the counts of reads in a moving window. |
| writeWiggle | writeWiggle writes a wiggle track or BigWig file suitable for uploading to the UCSC genome browser. |