Index

B | C | D | E | G | H | I | L | M | O | P | R | S | T | 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)
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_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.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_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)
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)
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)
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)

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)

T

tbitToBamChrName() (in module deeptools.utilities)
Tester (class in deeptools.countReadsPerBin)
(class in deeptools.SES_scaleFactor)
(class in deeptools.getScorePerBigWigBin)
toBytes() (in module deeptools.utilities)
toString() (in module deeptools.utilities)
trimZones() (in module deeptools.heatmapper)

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)