Index

B

BED_to_interval_tree() (in module deeptools.mapReduce) bedGraphToBigWig() (in module deeptools.writeBedGraph)

BedInterval (class in deeptools.readBed)

C

change_chrom_names() (deeptools.heatmapper.heatmapper static method) compute_correlation() (deeptools.correlation.Correlation method) compute_ratio() (in module deeptools.getRatio) compute_sub_matrix_worker() (deeptools.heatmapper.heatmapper static method) compute_sub_matrix_wrapper() (in module deeptools.heatmapper) computeCorrectedReadcounts() (in module deeptools.correctReadCounts) computeLambda() (in module deeptools.correctReadCounts) computeMatrix() (deeptools.heatmapper.heatmapper method) computePvalue() (in module deeptools.correctReadCounts) controlLambda() (in module deeptools.correctReadCounts)

copyFileInMemory() (in module deeptools.utilities) correctReadCounts() (in module deeptools.correctReadCounts) Correlation (class in deeptools.correlation) count_reads_in_region() (deeptools.countReadsPerBin.CountReadsPerBin method) countFragmentsInRegions_worker() (in module deeptools.getScorePerBigWigBin) countReadsInRegions_wrapper() (in module deeptools.countReadsPerBin) (in module deeptools.getScorePerBigWigBin) CountReadsPerBin (class in deeptools.countReadsPerBin) coverage_from_array() (deeptools.heatmapper.heatmapper static method) coverage_from_bam() (deeptools.heatmapper.heatmapper static method) coverage_from_big_wig() (deeptools.heatmapper.heatmapper static method)

D

deeptools (module) deeptools.bamHandler (module) deeptools.correctReadCounts (module) deeptools.correlation (module) deeptools.correlation_heatmap (module) deeptools.countReadsPerBin (module) deeptools.getFragmentAndReadSize (module) deeptools.getRatio (module) deeptools.getScorePerBigWigBin (module)

deeptools.heatmapper (module) deeptools.heatmapper_utilities (module) deeptools.mapReduce (module) deeptools.readBed (module) deeptools.SES_scaleFactor (module) deeptools.utilities (module) deeptools.writeBedGraph (module) deeptools.writeBedGraph_bam_and_bw (module)

E

estimateScaleFactor() (in module deeptools.SES_scaleFactor)

G

get_coverage_of_region() (deeptools.countReadsPerBin.CountReadsPerBin method) get_fragment_from_read() (deeptools.countReadsPerBin.CountReadsPerBin method) get_individual_matrices() (deeptools.heatmapper.heatmapper method) get_no_comment_line() (deeptools.readBed.ReadBed method) get_num_individual_matrix_cols() (deeptools.heatmapper.heatmapper method) get_outlier_indices() (deeptools.correlation.Correlation static method) get_read_and_fragment_length() (in module deeptools.getFragmentAndReadSize) get_regions_and_groups() (deeptools.heatmapper.heatmapper static method) get_values_from_line() (deeptools.readBed.ReadBed method) getChromSizes() (in module deeptools.getScorePerBigWigBin) getCommonChrNames() (in module deeptools.utilities) getCoverageFromBigwig() (in module deeptools.writeBedGraph_bam_and_bw) getFragmentLength_worker() (in module deeptools.getFragmentAndReadSize)

getFragmentLength_wrapper() (in module deeptools.getFragmentAndReadSize) getGC_content() (in module deeptools.utilities) getGenomeChunkLength() (in module deeptools.writeBedGraph) getProfileTicks() (in module deeptools.heatmapper_utilities) getRatio() (in module deeptools.getRatio) getRead() (deeptools.countReadsPerBin.Tester method) getReadLength() (deeptools.countReadsPerBin.CountReadsPerBin method) getScorePerBin() (in module deeptools.getScorePerBigWigBin) getSmoothRange() (deeptools.countReadsPerBin.CountReadsPerBin method) getTempFileName() (in module deeptools.utilities) getUserRegion() (in module deeptools.mapReduce) guess_file_type() (deeptools.readBed.ReadBed method)

H

heatmapper (class in deeptools.heatmapper)

L

load_matrix() (deeptools.correlation.Correlation method)

M

mapReduce() (in module deeptools.mapReduce) matrix_avg() (deeptools.heatmapper.heatmapper static method)

matrix_from_dict() (deeptools.heatmapper.heatmapper method) my_average() (deeptools.heatmapper.heatmapper static method)

N

next() (deeptools.readBed.ReadBed method)

O

openBam() (in module deeptools.bamHandler)

P

plot_correlation() (deeptools.correlation.Correlation method) (in module deeptools.correlation_heatmap) plot_pca() (deeptools.correlation.Correlation method)

plot_scatter() (deeptools.correlation.Correlation method) plot_single() (in module deeptools.heatmapper_utilities)

R

ratio() (in module deeptools.writeBedGraph) read_matrix_file() (deeptools.heatmapper.heatmapper method) ReadBed (class in deeptools.readBed) remove_outliers() (deeptools.correlation.Correlation method)

remove_row_of_zeros() (in module deeptools.countReadsPerBin) remove_rows_of_zeros() (deeptools.correlation.Correlation method) run() (deeptools.countReadsPerBin.CountReadsPerBin method) (deeptools.writeBedGraph.WriteBedGraph method)

S

save_BED() (deeptools.heatmapper.heatmapper method) save_corr_matrix() (deeptools.correlation.Correlation method) save_matrix() (deeptools.heatmapper.heatmapper method)

save_matrix_values() (deeptools.heatmapper.heatmapper method) saveTabulatedValues() (deeptools.heatmapper.heatmapper method) scaleCoverage() (in module deeptools.writeBedGraph)

T

tbitToBamChrName() (in module deeptools.utilities)

Tester (class in deeptools.countReadsPerBin) (class in deeptools.SES_scaleFactor) (class in deeptools.getScorePerBigWigBin)

W

which() (in module deeptools.utilities) WriteBedGraph (class in deeptools.writeBedGraph) writeBedGraph() (in module deeptools.writeBedGraph_bam_and_bw)

writeBedGraph_worker() (deeptools.writeBedGraph.WriteBedGraph method) (in module deeptools.writeBedGraph_bam_and_bw) writeBedGraph_wrapper() (in module deeptools.writeBedGraph) (in module deeptools.writeBedGraph_bam_and_bw)