API for valenlab/amplican
Automated analysis of CRISPR experiments

Global functions
$,AlignmentsExperimentSet-method Man page
AlignmentsExperimentSet Man page Source code
AlignmentsExperimentSet-class Man page
[,AlignmentsExperimentSet,numeric,missing,missing-method Man page
aa_frame Source code
alphabetQuality Man page Source code
amplican Man page
amplican-package Man page Man page
amplicanAlign Man page Source code
amplicanConsensus Man page Source code
amplicanFilter Man page Source code
amplicanMap Man page Source code
amplicanNormalize Man page Source code
amplicanOverlap Man page Source code
amplicanPipeline Man page Source code
amplicanReport Man page Source code
amplicanSummarize Man page Source code
amplican_print_reads Man page Source code
amplican_style Source code
amplican_xlim Source code
amplicon_primers Source code
annotate_with_amplicon Source code
as.list.AlignmentsExperimentSet Man page Source code
assignedCount Man page
assignedCount,AlignmentsExperimentSet-method Man page
barcodeData Man page
barcodeData,AlignmentsExperimentSet-method Man page
barcodeData<- Man page
barcodeData<-,AlignmentsExperimentSet-method Man page
c,AlignmentsExperimentSet-method Man page
cRamp Source code
cRampF Source code
checkConfigFile Man page Source code
checkFileWriteAccess Man page Source code
checkPrimers Man page Source code
checkTarget Man page Source code
cigarsToEvents Man page Source code
comb_along Man page Source code
cumsumw Man page Source code
decode Man page Source code
defGR Man page Source code
experimentData Man page
experimentData,AlignmentsExperimentSet-method Man page
experimentData<- Man page
experimentData<-,AlignmentsExperimentSet-method Man page
extractEvents Man page
extractEvents,AlignmentsExperimentSet-method Man page
findEOP Man page Source code
findLQR Man page Source code
findPD Man page Source code
flipRanges Man page Source code
fwdReads Man page
fwdReads,AlignmentsExperimentSet-method Man page
fwdReads<- Man page
fwdReads<-,AlignmentsExperimentSet-method Man page
fwdReadsType Man page
fwdReadsType,AlignmentsExperimentSet-method Man page
fwdReadsType<- Man page
fwdReadsType<-,AlignmentsExperimentSet-method Man page
getEventInfo Man page Source code
getEventInfoObj Source code
getEvents Man page Source code
getHits Source code
get_amplicon Man page Source code
get_left_primer Man page Source code
get_right_primer Man page Source code
ggplot_deletions Source code
ggplot_insertions Source code
ggplot_mismatches Source code
goodAvgQuality Man page Source code
goodBaseQuality Man page Source code
group_to_selection Source code
init Source code
is_hdr Source code
length,AlignmentsExperimentSet-method Man page
listClasses Source code
locate_pr_start Source code
lookupAlignment Man page
lookupAlignment,AlignmentsExperimentSet-method Man page
makeAlignment Man page Source code
merge_2_grobs Source code
merge_3_grobs Source code
merge_4_grobs Source code
metaplot_deletions Man page Source code
metaplot_insertions Man page Source code
metaplot_mismatches Man page Source code
mock_mm_df Source code
names,AlignmentsExperimentSet-method Man page
pairToEvents Man page Source code
plot_amplicon Man page Source code
plot_cuts Man page Source code
plot_deletions Man page Source code
plot_height Man page Source code
plot_heterogeneity Man page Source code
plot_insertions Man page Source code
plot_mismatches Man page Source code
plot_variants Man page Source code
range01 Source code Source code
readCounts Man page
readCounts,AlignmentsExperimentSet-method Man page
readCounts<- Man page
readCounts<-,AlignmentsExperimentSet-method Man page
return_metaplot Source code
return_plot Source code
revComp Man page Source code
rveReads Man page
rveReads,AlignmentsExperimentSet-method Man page
rveReads<- Man page
rveReads<-,AlignmentsExperimentSet-method Man page
rveReadsType Man page
rveReadsType,AlignmentsExperimentSet-method Man page
rveReadsType<- Man page
rveReadsType<-,AlignmentsExperimentSet-method Man page
scale_freq Source code
triangulate_ranges Source code
unassignedCount Man page
unassignedCount,AlignmentsExperimentSet-method Man page
unassignedData Man page
unassignedData,AlignmentsExperimentSet-method Man page
unassignedData<- Man page
unassignedData<-,AlignmentsExperimentSet-method Man page
upperGroups Man page Source code
writeAlignments Man page
writeAlignments,AlignmentsExperimentSet-method Man page
valenlab/amplican documentation built on June 18, 2018, 6:04 a.m.