deepTools
3.0.1
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Changes in deepTools2.0
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C
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D
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E
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G
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I
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M
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O
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P
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R
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S
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T
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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
chroms() (deeptools.deepBlue.deepBlue method)
close() (deeptools.deepBlue.deepBlue method)
compute_ratio() (in module deeptools.getRatio)
convertCmap() (in module deeptools.utilities)
copyFileInMemory() (in module deeptools.utilities)
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)
D
deepBlue (class in deeptools.deepBlue)
deeptools (module)
deeptools.bamHandler (module)
deeptools.correlation_heatmap (module)
deeptools.countReadsPerBin (module)
deeptools.deepBlue (module)
deeptools.getFragmentAndReadSize (module)
deeptools.getRatio (module)
deeptools.getScorePerBigWigBin (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_chunk_length() (deeptools.countReadsPerBin.CountReadsPerBin method)
get_coverage_of_region() (deeptools.countReadsPerBin.CountReadsPerBin method)
get_fragment_from_read() (deeptools.countReadsPerBin.CountReadsPerBin 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)
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)
getTLen() (in module deeptools.utilities)
getUserRegion() (in module deeptools.mapReduce)
gtfOptions() (in module deeptools.utilities)
I
is_proper_pair() (deeptools.countReadsPerBin.CountReadsPerBin static method)
isDeepBlue() (in module deeptools.deepBlue)
M
makeChromTiles() (in module deeptools.deepBlue)
makeRegions() (in module deeptools.deepBlue)
makeTiles() (in module deeptools.deepBlue)
mapReduce() (in module deeptools.mapReduce)
mergeRegions() (in module deeptools.deepBlue)
mungeChromosome() (in module deeptools.utilities)
O
openBam() (in module deeptools.bamHandler)
P
plot_correlation() (in module deeptools.correlation_heatmap)
preload() (deeptools.deepBlue.deepBlue method)
preloadWrapper() (in module deeptools.deepBlue)
R
ratio() (in module deeptools.writeBedGraph)
remove_row_of_zeros() (in module deeptools.countReadsPerBin)
run() (deeptools.countReadsPerBin.CountReadsPerBin method)
(deeptools.writeBedGraph.WriteBedGraph method)
S
scaleCoverage() (in module deeptools.writeBedGraph)
smartLabel() (in module deeptools.utilities)
smartLabels() (in module deeptools.utilities)
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)
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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