Deeptools原料药

deeptools由几个命令行和星系包装器组成，用于汇总可映射到参考基因组的下一代测序数据的信息。通过API，驱动deeptools命令的引擎也可以用于其他目的。

我们的 Deeptools API示例 逐步解释如何利用某些deeptools模块来实现deeptools套件范围之外的分析，例如计算特定基因组区域的读取数和计算frip分数。

• Deeptools API示例
  • 在区域中查找读取覆盖范围
  • 过滤读取
  • 基因组取样
  • 计算frip分数
  • 使用mapreduce对成对的末端片段长度进行采样
  • 索引和表格
• Deeptools软件包模块
  • Deeptools.ses？scaleFactor模块
    • Tester
    • estimateScaleFactor()
  • deeptools.bamhandler模块
    • countReadsInInterval()
    • getMappingStats()
    • openBam()
  • Deeptools.Correlation模块
    • Correlation
      • Correlation.compute_correlation()
      • Correlation.get_outlier_indices()
      • Correlation.load_matrix()
      • Correlation.plot_correlation()
      • Correlation.plot_pca()
      • Correlation.plot_scatter()
      • Correlation.plotly_correlation()
      • Correlation.plotly_pca()
      • Correlation.plotly_scatter()
      • Correlation.remove_outliers()
      • Correlation.remove_rows_of_zeros()
      • Correlation.save_corr_matrix()
  • deeptools.correlation_heatmap模块
    • plot_correlation()
  • deeptools.countreadsPerbin模块
    • CountReadsPerBin
      • CountReadsPerBin.count_reads_in_region()
      • CountReadsPerBin.getReadLength()
      • CountReadsPerBin.getSmoothRange()
      • CountReadsPerBin.get_chunk_length()
      • CountReadsPerBin.get_coverage_of_region()
      • CountReadsPerBin.get_fragment_from_read()
      • CountReadsPerBin.is_proper_pair()
      • CountReadsPerBin.run()
    • Tester
      • Tester.getRead()
    • countReadsInRegions_wrapper()
    • estimateSizeFactors()
    • remove_row_of_zeros()
  • deeptools.getfragmentandreadsize模块
    • getFragmentLength_worker()
    • getFragmentLength_wrapper()
    • get_read_and_fragment_length()
  • deeptools.getratio模块
    • compute_ratio()
    • getRatio()
  • deeptools.getscoreperbigwigbin模块
    • Tester
    • countFragmentsInRegions_worker()
    • countReadsInRegions_wrapper()
    • getChromSizes()
    • getScorePerBin()
  • Deeptools.Heatmapper模块
    • chopRegions()
    • chopRegionsFromMiddle()
    • computeSilhouetteScore()
    • compute_sub_matrix_wrapper()
    • heatmapper
      • heatmapper.change_chrom_names()
      • heatmapper.computeMatrix()
      • heatmapper.compute_sub_matrix_worker()
      • heatmapper.coverage_from_array()
      • heatmapper.coverage_from_big_wig()
      • heatmapper.getTicks()
      • heatmapper.get_individual_matrices()
      • heatmapper.get_num_individual_matrix_cols()
      • heatmapper.matrix_avg()
      • heatmapper.matrix_from_dict()
      • heatmapper.my_average()
      • heatmapper.read_matrix_file()
      • heatmapper.save_BED()
      • heatmapper.save_matrix()
      • heatmapper.save_matrix_values()
      • heatmapper.save_tabulated_values()
    • trimZones()
  • deeptools.heatmapper_实用程序模块
    • getProfileTicks()
    • plot_single()
    • plotly_single()
  • deeptools.mapreduce模块
    • blSubtract()
    • getUserRegion()
    • mapReduce()
  • deeptools.sumCoveragePerBin
    • SumCoveragePerBin
      • SumCoveragePerBin.get_coverage_of_region()
    • Tester
  • deeptools.utilities模块
    • bam_blacklisted_reads()
    • bam_blacklisted_worker()
    • bam_total_reads()
    • convertCmap()
    • copyFileInMemory()
    • getCommonChrNames()
    • getGC_content()
    • getTLen()
    • getTempFileName()
    • gtfOptions()
    • mungeChromosome()
    • smartLabel()
    • smartLabels()
    • tbitToBamChrName()
    • toBytes()
    • toString()
  • deeptools.writebedgraph模块
    • WriteBedGraph
      • WriteBedGraph.run()
      • WriteBedGraph.writeBedGraph_worker()
    • bedGraphToBigWig()
    • getGenomeChunkLength()
    • ratio()
    • scaleCoverage()
    • writeBedGraph_wrapper()
  • deeptools.writebedgraph_bam_和_bw模块
    • getCoverageFromBigwig()
    • writeBedGraph()
    • writeBedGraph_worker()
    • writeBedGraph_wrapper()
  • 模块内容

完整信息可在以下链接中找到： 索引 和 模块索引

deepTools Galaxy <http://deeptools.ie-freiburg.mpg.de> _.

code @ github <https://github.com/deeptools/deepTools/> _.