Man pages for pgpmartin/GeneNeighborhood
Analyze the Neighborhood (Upstream/Downstream Neighbors) of Genes

analyzeNeighborsDistanceAnalyze the distances to the upstream and downstream...
analyzeNeighborsOrientationAnalyze the orientation of gene neighbors for a set of...
annotationCoverageAroundFeaturesExtract stranded annotation profiles at and around a set of...
assembleProfilesAssemble profiles from the results of the...
binFeatureProfilesBin coverage profiles given as a matrix or RleList of...
extendPointPresenceExtend the presence value (1) of the closest single-point...
GenegrA GRanges with 676 random genes on a single chromosome
getAvgProfileWithCICompute the average profile and its confidence interval for a...
getCumulPercentProfilesFor gene sets, obtain the cumulative percentage of genes with...
getGeneNeighborhoodExtract info on upstream and downstream features/genes
getTESExtract the TES (=end of the gene) from a 'GRanges'
getTESregionExtract a region around the TES (=end of the gene) from a...
isBinaryMatTest if a matrix is a binary matrix
matrix2RleListConvert an 'matrix' to an 'RleList'
plotCumulPercentProfilePlot the cumulative proportions obtained from...
plotDistanceDistribplot the distribution of intergenic distances
plotMetageneAnnotProfilePlot metagene annotation profiles for different groups of...
plotNeighborsOrientationStacked barplot of gene orientations for upstream and...
profcompExtract windows of interest from a coverage.
RleList2matrixConvert an 'RleList' to a 'matrix'
statDistanceSideAnalyze intergenic distances
winsorizeMatrixWinsorizing of an entire matrix
pgpmartin/GeneNeighborhood documentation built on May 4, 2019, 6:40 p.m.