# Genome Intervals and Read Alignments for Functional Exploration

## Documentation for package ‘girafe’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

addNBSignificance | assess significance of sliding-window read counts
agiFromBam | Create AlignedGenomeIntervals objects from BAM files.
AlignedGenomeIntervals | Class 'AlignedGenomeIntervals'
AlignedGenomeIntervals-class | Class 'AlignedGenomeIntervals'
c-method | Class 'AlignedGenomeIntervals'
c.AlignedGenomeIntervals | Class 'AlignedGenomeIntervals'
chrlengths | Class 'AlignedGenomeIntervals'
chrlengths-method | Class 'AlignedGenomeIntervals'
chrlengths<- | Class 'AlignedGenomeIntervals'
chrlengths<--method | Class 'AlignedGenomeIntervals'
chromosome-method | Class 'AlignedGenomeIntervals'
clusters-method | Class 'AlignedGenomeIntervals'
coerce-method | Class 'AlignedGenomeIntervals'
countReadsAnnotated | Sum up aligned reads per category of genome feature
coverage-method | Class 'AlignedGenomeIntervals'
detail-method | Class 'AlignedGenomeIntervals'
estimateNBParams | assess significance of sliding-window read counts
export | Class 'AlignedGenomeIntervals'
export-method | Class 'AlignedGenomeIntervals'
extend | Class 'AlignedGenomeIntervals'
extend-method | Class 'AlignedGenomeIntervals'
fracOverlap | Retrieve intervals overlapping by fraction of width
hist-method | Class 'AlignedGenomeIntervals'
id-method | Class 'AlignedGenomeIntervals'
id<- | Class 'AlignedGenomeIntervals'
id<--method | Class 'AlignedGenomeIntervals'
interval_included-method | Class 'AlignedGenomeIntervals'
interval_overlap-method | Class 'AlignedGenomeIntervals'
intPhred | Extract integer Phred score values from FastQ data
matches | Class 'AlignedGenomeIntervals'
matches-method | Class 'AlignedGenomeIntervals'
matches<- | Class 'AlignedGenomeIntervals'
matches<--method | Class 'AlignedGenomeIntervals'
medianByPosition | Compute median quality for each nucleotide position
nchar-method | Class 'AlignedGenomeIntervals'
organism-method | Class 'AlignedGenomeIntervals'
organism<- | Class 'AlignedGenomeIntervals'
organism<--method | Class 'AlignedGenomeIntervals'
perWindow | Investigate aligned reads in genome intervals with sliding windows
plot-method | Class 'AlignedGenomeIntervals'
reads | Class 'AlignedGenomeIntervals'
reads-method | Class 'AlignedGenomeIntervals'
reads<- | Class 'AlignedGenomeIntervals'
reads<--method | Class 'AlignedGenomeIntervals'
reduce-method | Class 'AlignedGenomeIntervals'
sample-method | Class 'AlignedGenomeIntervals'
score-method | Class 'AlignedGenomeIntervals'
score<- | Class 'AlignedGenomeIntervals'
score<--method | Class 'AlignedGenomeIntervals'
seq_name | Class 'AlignedGenomeIntervals'
seq_name-method | Class 'AlignedGenomeIntervals'
show-method | Class 'AlignedGenomeIntervals'
sort-method | Class 'AlignedGenomeIntervals'
strand-method | Class 'AlignedGenomeIntervals'
strand<--method | Class 'AlignedGenomeIntervals'
subset | Class 'AlignedGenomeIntervals'
subset-method | Class 'AlignedGenomeIntervals'
summary | Class 'AlignedGenomeIntervals'
summary-method | Class 'AlignedGenomeIntervals'
trimAdapter | Remove 3' adapter contamination
which_nearest | Methods for function 'which_nearest' and genome intervals
which_nearest-method | Methods for function 'which_nearest' and genome intervals
width-method | Class 'AlignedGenomeIntervals'
[-method | Class 'AlignedGenomeIntervals'