Man pages for kevincjnixon/ChIPATAC
Wrapper functions for useful genomic analyses like ChIP-seq or ATAC-seq.
| addSym | Provide gene symbols for transcripts in metaList |
| aggrAcc | Aggregate peak counts to gene features |
| chrHeatMap | Plot a heatmap of binned signal across the whole genome |
| chrHeatMat | Average signal across the genome in bins for a list of... |
| compHOMER | Function to compare two sets of HOMER known motif enrichment... |
| customGREAT | Function to perform GREAT analysis using custom gene sets |
| FeatureEnrichment | Calculate empirical p-value for genomic feature enrichment |
| getAnnoGenes | Subset and extract genes from ChIPseeker annotations |
| makeCovList | Function to import coverage matrix to R |
| plotMetaGene | Make a custom metagene plot |
| plotVenn_gr | Function to plot Venn diagram of overlapping peaks |
| readBed | Function to read tab-delimited bed file to GenomicRanges... |
| readBed2 | Read a bed file to genomicRanges Object with option for... |
| retRegion | Return genomic regions associated with a specific gene or set... |
| scalefun | Scale the upstream/downstream regions of a coverage matrix to... |
| scaleMeta | Apply the scalefun() to a metalist |
| writeBETA | Function to export GenomicRanges object for use with Cistrome... |
| writeGTF | Function to export GenomicRanges to GTF format |
