Index

_

__init__() (metaseq._genomic_signal.BamSignal method) (metaseq._genomic_signal.BaseSignal method) (metaseq._genomic_signal.BedSignal method) (metaseq._genomic_signal.BigBedSignal method) (metaseq._genomic_signal.BigWigSignal method) (metaseq._genomic_signal.IntervalSignal method) (metaseq.filetype_adapters.BamAdapter method) (metaseq.filetype_adapters.BaseAdapter method) (metaseq.filetype_adapters.BedAdapter method) (metaseq.filetype_adapters.BigBedAdapter method) (metaseq.filetype_adapters.BigWigAdapter method) (metaseq.integration.chipseq.Chipseq method) (metaseq.minibrowser.BaseMiniBrowser method) (metaseq.minibrowser.GeneModelMiniBrowser method) (metaseq.minibrowser.SignalMiniBrowser method) (metaseq.plotutils.MarginalHistScatter method) (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.LazyDict method) (metaseq.results_table.ResultsTable method)

_local_count() (in module metaseq.array_helpers) _local_coverage() (in module metaseq.array_helpers)

A

add_labels_to_subsets() (in module metaseq.plotutils) add_legends() (metaseq.plotutils.MarginalHistScatter method) align_with() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.ResultsTable method) append() (metaseq.plotutils.MarginalHistScatter method) array() (metaseq._genomic_signal.BamSignal method) (metaseq._genomic_signal.BaseSignal method) (metaseq._genomic_signal.BedSignal method) (metaseq._genomic_signal.BigBedSignal method) (metaseq._genomic_signal.BigWigSignal method) (metaseq._genomic_signal.IntervalSignal method)

attach_db() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.ResultsTable method) autosql_file() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method)

B

BamAdapter (class in metaseq.filetype_adapters) BamSignal (class in metaseq._genomic_signal) BaseAdapter (class in metaseq.filetype_adapters) BaseMiniBrowser (class in metaseq.minibrowser) BaseSignal (class in metaseq._genomic_signal)

BedAdapter (class in metaseq.filetype_adapters) BedSignal (class in metaseq._genomic_signal) BigBedAdapter (class in metaseq.filetype_adapters) BigBedSignal (class in metaseq._genomic_signal) BigWigAdapter (class in metaseq.filetype_adapters) BigWigSignal (class in metaseq._genomic_signal)

C

calculate_limits() (in module metaseq.plotutils) callback() (metaseq.integration.chipseq.Chipseq method) changed() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) Chipseq (class in metaseq.integration.chipseq) ci() (in module metaseq.plotutils) ci_plot() (in module metaseq.plotutils) close_all() (metaseq.minibrowser.BaseMiniBrowser method) (metaseq.minibrowser.GeneModelMiniBrowser method) (metaseq.minibrowser.SignalMiniBrowser method)

clustered_sortind() (in module metaseq.plotutils) cmap_center_adjust() (in module metaseq.colormap_adjust) cmap_center_point_adjust() (in module metaseq.colormap_adjust) cmap_powerlaw_adjust() (in module metaseq.colormap_adjust) color_test() (in module metaseq.colormap_adjust) colormapped_bedfile() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) compare() (in module metaseq.integration.signal_comparison)

D

DESeq2Results (class in metaseq.results_table) DESeqResults (class in metaseq.results_table) diff_array() (metaseq.integration.chipseq.Chipseq method) disenriched() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method)

downregulated() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method)

E

EdgeRResults (class in metaseq.results_table) enriched() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method)

example_panel() (metaseq.minibrowser.BaseMiniBrowser method) (metaseq.minibrowser.GeneModelMiniBrowser method) (metaseq.minibrowser.SignalMiniBrowser method)

F

features() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.ResultsTable method)

five_prime() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.ResultsTable method)

G

gene_panel() (metaseq.minibrowser.GeneModelMiniBrowser method) GeneModelMiniBrowser (class in metaseq.minibrowser) genes_in_common() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.ResultsTable method)

genes_with_peak() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.ResultsTable method) genome() (metaseq._genomic_signal.BamSignal method) genomic_signal() (in module metaseq._genomic_signal)

I

imshow() (in module metaseq.plotutils)

input_ip_plots() (in module metaseq.plotutils) IntervalSignal (class in metaseq._genomic_signal)

L

LazyDict (class in metaseq.results_table) local_count() (metaseq._genomic_signal.BamSignal method) (metaseq._genomic_signal.BedSignal method) (metaseq._genomic_signal.BigBedSignal method) (metaseq._genomic_signal.IntervalSignal method)

local_coverage() (metaseq._genomic_signal.BamSignal method) (metaseq._genomic_signal.BaseSignal method) (metaseq._genomic_signal.BedSignal method) (metaseq._genomic_signal.BigBedSignal method) (metaseq._genomic_signal.BigWigSignal method) (metaseq._genomic_signal.IntervalSignal method)

M

ma_plot() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) make_fig() (metaseq.minibrowser.BaseMiniBrowser method) (metaseq.minibrowser.GeneModelMiniBrowser method) (metaseq.minibrowser.SignalMiniBrowser method) mapped_read_count() (metaseq._genomic_signal.BamSignal method) MarginalHistScatter (class in metaseq.plotutils)

matrix_and_line_shell() (in module metaseq.plotutils) metaseq._genomic_signal (module) metaseq.array_helpers (module) metaseq.colormap_adjust (module) metaseq.filetype_adapters (module) metaseq.integration (module) metaseq.minibrowser (module) metaseq.plotutils (module) metaseq.results_table (module)

N

nice_log() (in module metaseq.plotutils)

P

panels() (metaseq.minibrowser.BaseMiniBrowser method) (metaseq.minibrowser.GeneModelMiniBrowser method) (metaseq.minibrowser.SignalMiniBrowser method) plot() (metaseq.integration.chipseq.Chipseq method) (metaseq.minibrowser.BaseMiniBrowser method) (metaseq.minibrowser.GeneModelMiniBrowser method) (metaseq.minibrowser.SignalMiniBrowser method)

prepare_logged() (in module metaseq.plotutils)

R

radviz() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.ResultsTable method)

reindex_to() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.ResultsTable method) ResultsTable (class in metaseq.results_table)

S

scatter() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.ResultsTable method) signal_panel() (metaseq.minibrowser.GeneModelMiniBrowser method) (metaseq.minibrowser.SignalMiniBrowser method)

SignalMiniBrowser (class in metaseq.minibrowser) smart_colormap() (in module metaseq.colormap_adjust) strip_unknown_features() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.ResultsTable method) supported_formats() (in module metaseq._genomic_signal)

T

three_prime() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.ResultsTable method) tip_fdr() (in module metaseq.plotutils) tip_zscores() (in module metaseq.plotutils) TSS() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.ResultsTable method)

TTS() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.ResultsTable method)

U

unchanged() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) update() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method) (metaseq.results_table.ResultsTable method)

upregulated() (metaseq.results_table.DESeq2Results method) (metaseq.results_table.DESeqResults method) (metaseq.results_table.EdgeRResults method)