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
- Deeptools软件包模块
- Deeptools.ses?scaleFactor模块
- deeptools.bamhandler模块
- 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
- deeptools.countreadsPerbin模块
- deeptools.getfragmentandreadsize模块
- deeptools.getratio模块
- deeptools.getscoreperbigwigbin模块
- 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
- deeptools.mapreduce模块
- deeptools.sumCoveragePerBin
- deeptools.utilities模块
- deeptools.writebedgraph模块
- deeptools.writebedgraph_bam_和_bw模块
- 模块内容
deepTools Galaxy <http://deeptools.ie-freiburg.mpg.de> _. |
code @ github <https://github.com/deeptools/deepTools/> _. |