DOTSeq-package	DOTSeq
.PostHoc	PostHoc-class
annotate_orf_type	annotate_orf_type
assign_strategy_levels	assign_strategy_levels
bm_use_ensembl	bm_use_ensembl
calculateTE	calculateTE
calculateUsage	calculateUsage
calculate_mean_dispersion	calculate_mean_dispersion
cistronic_data	cistronic_data
contrast_vectors	contrast_vectors
countReads	countReads
create_datasets	create_datasets
create_read_numbers	create_read_numbers
DOTSeq	DOTSeq
DOTSeqDataSets-class	DOTSeqDataSets-class
DOTSeqDataSetsFromFeatureCounts	DOTSeqDataSets
DOTSeqDataSetsFromSummarizeOverlaps	DOTSeqDataSets
DOUData-class	DOUData-class
DOUData-validity	DOUData-validity
DTEData-class	DTEData-class
extract_results	extract_results
filter_gtf	filter_gtf
findORFsFasta	findORFsFasta
fitDOU	fitDOU
fitResults	PostHoc-accessors
fitResults,PostHoc-method	PostHoc-accessors
fit_beta_binomial	fit_beta_binomial
fit_glmm	fit_glmm
fmla	fmla-method
fmla,DOUData-method	fmla-method
fmla,DTEData-method	fmla-method
generate_coefficients	generate_coefficients
getContrasts	getContrasts-method
getContrasts,DOTSeqDataSets-method	getContrasts-method
getContrasts,DOUData-method	getContrasts-method
getContrasts,DTEData-method	getContrasts-method
getContrasts<-	getContrasts-method
getContrasts<-,DOUData-method	getContrasts-method
getContrasts<-,DTEData-method	getContrasts-method
getDOU	getDOU-method
getDOU,DOTSeqDataSets-method	getDOU-method
getDOU<-	getDOU-method
getDOU<-,DOTSeqDataSets-method	getDOU-method
getDTE	getDTE-method
getDTE,DOTSeqDataSets-method	getDTE-method
getDTE<-	getDTE-method
getDTE<-,DOTSeqDataSets-method	getDTE-method
getExonicReads	getExonicReads
getORFs	getORFs
get_lfsr_annotation	get_lfsr_annotation
get_params	get_params
get_significant_genes	get_significant_genes
group_bam_files	group_bam_files
gSort	gSort
is_paired_end	is_paired_end
lastExonEndPerGroup	lastExonEndPerGroup
lastExonPerGroup	lastExonPerGroup
lastExonStartPerGroup	lastExonStartPerGroup
longestORFs	longestORFs
mapIDs	mapIDs
match_runs	match_runs
modelType	PostHoc-accessors
modelType,PostHoc-method	PostHoc-accessors
numExonsPerGroup	numExonsPerGroup
parse_condition_table	parse_condition_table
plotDOT	plotDOT
plot_composite	plot_composite
plot_heatmap	plot_heatmap
plot_orf_usage	plot_orf_usage
plot_pca	plot_pca
plot_venn	plot_venn
plot_volcano	plot_volcano
PostHoc	PostHoc
posthoc	PostHoc-accessors
posthoc,PostHoc-method	PostHoc-accessors
PostHoc-class	PostHoc-class
reduce_formula	reduce_formula
remove_random_effects	remove_random_effects
reset_graphics	reset_graphics
reverseMinusStrandPerGroup	reverseMinusStrandPerGroup
runtime	runtime
run_diagnostic	run_diagnostic
seqnamesPerGroup	seqnamesPerGroup
show,DOTSeqDataSets-method	DOTSeqDataSets-class
simDOT	simDOT
sortPerGroup	sortPerGroup
specs	specs-method
specs,DOUData-method	specs-method
specs,DTEData-method	specs-method
stopSites	stopSites
strandBool	strandBool
strandPerGroup	strandPerGroup
testDOU	testDOU
widthPerGroup	widthPerGroup
