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C
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D
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E
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H
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I
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L
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M
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O
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P
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R
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W
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)
chroms() (deeptools.deepBlue.deepBlue method)
close() (deeptools.deepBlue.deepBlue 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)
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
deepBlue (class in deeptools.deepBlue)
deeptools (module)
deeptools.bamHandler (module)
deeptools.correlation (module)
deeptools.correlation_heatmap (module)
deeptools.countReadsPerBin (module)
deeptools.deepBlue (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)
getChroms() (deeptools.deepBlue.deepBlue method)
getChromSizes() (in module deeptools.getScorePerBigWigBin)
getCommonChrNames() (in module deeptools.utilities)
getCoverageFromBigwig() (in module deeptools.writeBedGraph_bam_and_bw)
getEID() (deeptools.deepBlue.deepBlue method)
getFragmentLength_worker() (in module deeptools.getFragmentAndReadSize)
getFragmentLength_wrapper() (in module deeptools.getFragmentAndReadSize)
getGC_content() (in module deeptools.utilities)
getGenome() (deeptools.deepBlue.deepBlue method)
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)
isDeepBlue() (in module deeptools.deepBlue)
L
load_matrix() (deeptools.correlation.Correlation method)
M
makeChromTiles() (in module deeptools.deepBlue)
makeRegions() (in module deeptools.deepBlue)
makeTiles() (in module deeptools.deepBlue)
mapReduce() (in module deeptools.mapReduce)
matrix_avg() (deeptools.heatmapper.heatmapper static method)
matrix_from_dict() (deeptools.heatmapper.heatmapper method)
mergeRegions() (in module deeptools.deepBlue)
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)
preload() (deeptools.deepBlue.deepBlue method)
preloadWrapper() (in module deeptools.deepBlue)
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.SES_scaleFactor)
(class in deeptools.getScorePerBigWigBin)
(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)
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