| TransView-package | Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets. |
| annotatePeaks | Associates peaks to TSS |
| chromosomes | Class '"DensityContainer"' |
| chromosomes-method | Class '"DensityContainer"' |
| class:DensityContainer | Class '"DensityContainer"' |
| class:TVResults | Class '"TVResults"' |
| clusters | Class '"TVResults"' |
| clusters-method | Class '"TVResults"' |
| cluster_order | Class '"TVResults"' |
| cluster_order-method | Class '"TVResults"' |
| collapsed | Class '"DensityContainer"' |
| collapsed-method | Class '"DensityContainer"' |
| compression | Class '"DensityContainer"' |
| compression-method | Class '"DensityContainer"' |
| data_pointer | Class '"DensityContainer"' |
| data_pointer-method | Class '"DensityContainer"' |
| DensityContainer-class | Class '"DensityContainer"' |
| env | Class '"DensityContainer"' |
| env-method | Class '"DensityContainer"' |
| ex_name | Class '"DensityContainer"' |
| ex_name-method | Class '"DensityContainer"' |
| ex_name<- | Class '"DensityContainer"' |
| ex_name<--method | Class '"DensityContainer"' |
| filtered | Class '"DensityContainer"' |
| filtered-method | Class '"DensityContainer"' |
| filtered_reads | Class '"DensityContainer"' |
| filtered_reads-method | Class '"DensityContainer"' |
| fmapmass | Class '"DensityContainer"' |
| fmapmass-method | Class '"DensityContainer"' |
| gcoverage | Class '"DensityContainer"' |
| gcoverage-method | Class '"DensityContainer"' |
| gsize | Class '"DensityContainer"' |
| gsize-method | Class '"DensityContainer"' |
| gtf2gr | GTF file parsing |
| histogram | Histogram of the read distribution |
| histogram-method | Histogram of the read distribution |
| histogram-methods | Histogram of the read distribution |
| lcoverage | Class '"DensityContainer"' |
| lcoverage-method | Class '"DensityContainer"' |
| lmaxScore | Class '"DensityContainer"' |
| lmaxScore-method | Class '"DensityContainer"' |
| lowqual | Class '"DensityContainer"' |
| lowqual-method | Class '"DensityContainer"' |
| lsize | Class '"DensityContainer"' |
| lsize-method | Class '"DensityContainer"' |
| macs2gr | Convenience function for MACS output conversion |
| maxScore | Class '"DensityContainer"' |
| maxScore-method | Class '"DensityContainer"' |
| meltPeak | Convenience function which returns a data frame with normalized peak densities suitable for plotting with ggplot2 |
| neg | Class '"DensityContainer"' |
| neg-method | Class '"DensityContainer"' |
| nreads | Class '"DensityContainer"' |
| nreads-method | Class '"DensityContainer"' |
| origin | Class '"DensityContainer"' |
| origin-method | Class '"DensityContainer"' |
| paired | Class '"DensityContainer"' |
| paired-method | Class '"DensityContainer"' |
| paired_reads | Class '"DensityContainer"' |
| paired_reads-method | Class '"DensityContainer"' |
| parameters | Class '"TVResults"' |
| parameters-method | Class '"TVResults"' |
| parseReads | User configurable efficient assembly of read density maps |
| peak2tss | Changes the peak center to the next TSS according to previous annotation |
| plotTV | Plot and cluster global read densities |
| plotTVData | Summarize plotTV results |
| plotTVData,TVResults | Summarize plotTV results |
| plotTVData-method | Summarize plotTV results |
| plotTVData-methods | Summarize plotTV results |
| pos | Class '"DensityContainer"' |
| pos-method | Class '"DensityContainer"' |
| proper_pairs | Class '"DensityContainer"' |
| proper_pairs-method | Class '"DensityContainer"' |
| readthrough_pairs | Class '"DensityContainer"' |
| readthrough_pairs-method | Class '"DensityContainer"' |
| rmTV | Free space occupied by DensityContainer |
| rmTV-method | Free space occupied by DensityContainer |
| rmTV-methods | Free space occupied by DensityContainer |
| scores_peaks | Class '"TVResults"' |
| scores_peaks-method | Class '"TVResults"' |
| scores_rna | Class '"TVResults"' |
| scores_rna-method | Class '"TVResults"' |
| show-method | Class '"DensityContainer"' |
| show-method | Class '"TVResults"' |
| size | Class '"DensityContainer"' |
| size-method | Class '"DensityContainer"' |
| slice1 | Slice read densities from a TransView dataset |
| slice1-method | Slice read densities from a TransView dataset |
| slice1-methods | Slice read densities from a TransView dataset |
| slice1T | Slice read densities of whole transcripts from a TransView DensityContainer |
| slice1T-method | Slice read densities of whole transcripts from a TransView DensityContainer |
| slice1T-methods | Slice read densities of whole transcripts from a TransView DensityContainer |
| sliceN | Slice read densities from a TransView dataset |
| sliceN-method | Slice read densities from a TransView dataset |
| sliceN-methods | Slice read densities from a TransView dataset |
| sliceNT | Slice read densities of whole transcripts from a TransView DensityContainer |
| sliceNT-method | Slice read densities of whole transcripts from a TransView DensityContainer |
| sliceNT-methods | Slice read densities of whole transcripts from a TransView DensityContainer |
| spliced | Class '"DensityContainer"' |
| spliced-method | Class '"DensityContainer"' |
| spliced<- | Class '"DensityContainer"' |
| spliced<--method | Class '"DensityContainer"' |
| strands | Class '"DensityContainer"' |
| strands-method | Class '"DensityContainer"' |
| summaryTV | Class '"TVResults"' |
| summaryTV-method | Class '"TVResults"' |
| TransView | Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets. |
| TVResults-class | Class '"TVResults"' |
| tvStats | DensityContainer accessor function |
| tvStats-method | DensityContainer accessor function |
| tvStats-methods | DensityContainer accessor function |