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 |