Index

B

bam_blacklisted_reads() (in module deeptools.utilities) bam_blacklisted_worker() (in module deeptools.utilities)

bam_total_reads() (in module deeptools.utilities) bedGraphToBigWig() (in module deeptools.writeBedGraph) blSubtract() (in module deeptools.mapReduce)

C

change_chrom_names() (deeptools.heatmapper.heatmapper static method) chopRegions() (in module deeptools.heatmapper) chopRegionsFromMiddle() (in module deeptools.heatmapper) 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) computeMatrix() (deeptools.heatmapper.heatmapper method) computeSilhouetteScore() (in module deeptools.heatmapper) convertCmap() (in module deeptools.utilities)

copyFileInMemory() (in module deeptools.utilities) Correlation (class in deeptools.correlation) count_reads_in_region() (deeptools.countReadsPerBin.CountReadsPerBin method) countFragmentsInRegions_worker() (in module deeptools.getScorePerBigWigBin) countReadsInInterval() (in module deeptools.bamHandler) 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_big_wig() (deeptools.heatmapper.heatmapper static method)

D

deeptools module deeptools.bamHandler 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.SES_scaleFactor module deeptools.sumCoveragePerBin module deeptools.utilities module deeptools.writeBedGraph module deeptools.writeBedGraph_bam_and_bw module

E

estimateScaleFactor() (in module deeptools.SES_scaleFactor)

estimateSizeFactors() (in module deeptools.countReadsPerBin)

G

get_chunk_length() (deeptools.countReadsPerBin.CountReadsPerBin method) get_coverage_of_region() (deeptools.countReadsPerBin.CountReadsPerBin method) (deeptools.sumCoveragePerBin.SumCoveragePerBin method) get_fragment_from_read() (deeptools.countReadsPerBin.CountReadsPerBin method) get_individual_matrices() (deeptools.heatmapper.heatmapper 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) 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) getMappingStats() (in module deeptools.bamHandler) 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) getTicks() (deeptools.heatmapper.heatmapper method) getTLen() (in module deeptools.utilities) getUserRegion() (in module deeptools.mapReduce) gtfOptions() (in module deeptools.utilities)

H

heatmapper (class in deeptools.heatmapper)

I

is_proper_pair() (deeptools.countReadsPerBin.CountReadsPerBin static method)

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) module deeptools deeptools.bamHandler deeptools.correlation deeptools.correlation_heatmap deeptools.countReadsPerBin deeptools.getFragmentAndReadSize deeptools.getRatio deeptools.getScorePerBigWigBin deeptools.heatmapper deeptools.heatmapper_utilities deeptools.mapReduce deeptools.SES_scaleFactor deeptools.sumCoveragePerBin deeptools.utilities deeptools.writeBedGraph deeptools.writeBedGraph_bam_and_bw

mungeChromosome() (in module deeptools.utilities) my_average() (deeptools.heatmapper.heatmapper static 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) plotly_correlation() (deeptools.correlation.Correlation method) plotly_pca() (deeptools.correlation.Correlation method) plotly_scatter() (deeptools.correlation.Correlation method) plotly_single() (in module deeptools.heatmapper_utilities)

R

ratio() (in module deeptools.writeBedGraph) read_matrix_file() (deeptools.heatmapper.heatmapper method) 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)

save_tabulated_values() (deeptools.heatmapper.heatmapper method) scaleCoverage() (in module deeptools.writeBedGraph) smartLabel() (in module deeptools.utilities) smartLabels() (in module deeptools.utilities) SumCoveragePerBin (class in deeptools.sumCoveragePerBin)

T

tbitToBamChrName() (in module deeptools.utilities) Tester (class in deeptools.countReadsPerBin) (class in deeptools.getScorePerBigWigBin) (class in deeptools.SES_scaleFactor) (class in deeptools.sumCoveragePerBin)

toBytes() (in module deeptools.utilities) toString() (in module deeptools.utilities) trimZones() (in module deeptools.heatmapper)

W

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)