deepTools API — deepTools 3.5.6 documentation (original) (raw)
deepTools consists of several command line and Galaxy wrappers for summarizing the information of Next Generation Sequencing data that can be mapped to a reference genome. Through the API, the engine powering the deepTools commands can be used for other purposes as well.
Our deepTools API example explains step-by-step how to make use of some deepTools modules to achieve analyses outside the scope of the deepTools suite such as counting reads for certain genome regions and computing the FRiP score.
- deepTools API example
- deeptools package modules
- deeptools.SES_scaleFactor module
* Tester
* estimateScaleFactor() - deeptools.bamHandler module
* countReadsInInterval()
* getMappingStats()
* openBam() - deeptools.correlation module
* 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 module
* plot_correlation() - deeptools.countReadsPerBin module
* 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 module
* getFragmentLength_worker()
* getFragmentLength_wrapper()
* get_read_and_fragment_length() - deeptools.getRatio module
* compute_ratio()
* getRatio() - deeptools.getScorePerBigWigBin module
* Tester
* countFragmentsInRegions_worker()
* countReadsInRegions_wrapper()
* getChromSizes()
* getScorePerBin() - deeptools.heatmapper module
* 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_utilities module
* getProfileTicks()
* plot_single()
* plotly_single() - deeptools.mapReduce module
* blSubtract()
* getUserRegion()
* mapReduce() - deeptools.sumCoveragePerBin
* SumCoveragePerBin
* SumCoveragePerBin.get_coverage_of_region()
* Tester - deeptools.utilities module
* 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 module
* WriteBedGraph
* WriteBedGraph.run()
* WriteBedGraph.writeBedGraph_worker()
* bedGraphToBigWig()
* getGenomeChunkLength()
* ratio()
* scaleCoverage()
* writeBedGraph_wrapper() - deeptools.writeBedGraph_bam_and_bw module
* getCoverageFromBigwig()
* writeBedGraph()
* writeBedGraph_worker()
* writeBedGraph_wrapper() - Module contents
- deeptools.SES_scaleFactor module
Complete information can be found in the following links: Index and Module Index