Genome Intervals and Read Alignments for Functional Exploration

Documentation for package ‘girafe’ version 1.4.0

DESCRIPTION file.
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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-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'