Man pages for rpolicastro/tsrexplorer
TSS and TSR Analysis

annotate_featuresAnnotate Features
apply_thresholdApply a threshold to TSSs or TSRs
associate_with_tsrAssociate TSSs
common_paramsFunction to hold common parameters.
conditionalsData Conditions Input
condition_dataData Conditionals
differential_expressionAnalyze Differential Features
dot-count_featuresCalculate Feature Counts
dot-count_matrixGenerate Count Matrix.
dot-de_statusMark DE Status
dot-out_of_bounds_indexGet index of out of bounds ranges.
dot-prepare_annotationPrepare Genome Annotation
dot-prepare_assemblyPrepare Genome Assembly
export_for_enrichmentExport to clusterProfiler
extract_counts-functionExtract Counts
extract_de-functionExtract Differential Gene Sets
extract_matrix-functionExtract Count Matrices
fit_de_modelDifferential feature analysis
format_countsFormat Counts
G_correctionCorrect G artifact
gene_tracksGene Tracks
get_annotationGet Genome Annotation
get_assemblyGet Genome Assembly
get_countsGet TSS or TSR count tables.
get_diff_modelGet Differential TSS/TSR models
get_diff_resultsGet Differential TSS/TSR results
get_grangesGet TSS or TSR GRanges.
get_sample_sheetGet Sample Sheet
get_shifting_resultsGet Shifting Results
import_bamsImport BAMs
mark_dominantMark Dominant
merge_samplesMerge Samples
normalize_countsNormalize TSS counts
orderingOrdering
pipePipe operator
plot_correlationPlot Sample Correlation
plot_densityDensity Plots
plot_detected_featuresGenes/Transcripts Detected
plot_dinucleotide_frequenciesDinucleotide Analysis
plot_genomic_distributionGenomic Distribution
plot_heatmapPlot Heatmap
plot_maMA Plot
plot_num_dePlot DE Numbers
plot_reductionDimensionality Reduction.
plot_sequence_colormapPlot Sequence Color Map
plot_sequence_logoGenerate Sequence Logo
plot_shift_countShift Count Plot
plot_shift_rankShifting Rank Plot
plot_threshold_explorationPlot Threshold Exploration
plot_tsr_metricPlot TSR Metrics
plot_volcanoVolcano Plot
preliminary_filterPreliminary Filter
quantilingQuantiling
retrieve_seqsRetrieve Sequences
set_slot-functionSet Slot Data
ShiftScores-functionShift Score
softclip_compositionComposition of Soft-clipped Bases
softclip_histogramNumber of soft-clipped bases.
tsr_experiment-genericAdd TSRs
tsr_explorer-classTSRexploreR Class
tsr_exportExport TSRs
tsr_importImport TSRs
tsr_metricsTSR Metrics
tss_aggregateAggregate TSSs
tss_clusteringTSS Clustering
tss_experiment-genericAdd TSSs
tss_exportExport TSSs
tss_importImport TSSs
TSSsYeast STRIPE-seq TSSs
tss_shiftTSS Shifting
TSSs_reducedSTRIPE-seq TSSs YDR077W (Diamide)
rpolicastro/tsrexplorer documentation built on Oct. 17, 2021, 3:02 p.m.