·computeMatrix ·对基因区域以及上下游划bin,计算每个bin内Chip的信号强度 ·用法: ·computeMatrixscale-regions-SG_K4me3_1.bw G_K27ac_1.bw G_K4ME1_1.bw G_K27me3 D_K4me3_1.bw D_K27ac_1.bw D_K4ME1_1.bw D_K27me3-Rup.Gene.bed down.Gene.bed–beforeRegionStartLength5000--regionBo...
bamCompare与bamCoverage 功能相似,只是bamCompare是基于两个bam文件的比较bigwigComparebigwigCompare也是针对于两个bigwig文件,将基因组以划bin的形式,计算这两个bigwig文件在每个bin覆盖深度的比值computeMatrix此模块主要为后期的数据可视化模块plotHeatmap and plotProfiles.服务,针对bigWig文件,它用来计算对基因区域以及...
56 - parents=[computeMatrixRequiredArgs(), 57 - computeMatrixOutputArgs(), 58 - computeMatrixOptArgs(case='scale-regions'), 59 - parserCommon.gtf_options(), 60 - dbParser], 47 + parents=[ 48 + computeMatrixRequiredArgs(), 49 + computeMatrixOutputArgs(), 50 + computeMatrixOptAr...
2.0.1 bin config deeptools dist docs content tools test_plots bamCompare.rst bamCoverage.rst bamPEFragmentSize.rst bigwigCompare.rst computeGCBias.rst computeMatrix.rst correctGCBias.rst multiBamSummary.rst multiBigwigSummary.rst plotCorrelation.rst plotCoverage.rst plotFingerprint.rst plotHeatmap....
computeMatrix 此模块主要为后期的数据可视化模块plotHeatmapandplotProfiles.服务,针对bigWig文件,它用来计算对基因区域以及上下游划bin,计算每个bin内ChIP的信号强度 其次Deeptools可以对数据进行质控 plotCorrelation 主要是针对multiBamSummary 产生的矩阵,利用pearson 或者spearman 计算样本间的相关性 ...
For more details on the optional output, see the examples for computeMatrix. Usage examples The following example creates a heatmap over hg19 transcripts for our test ENCODE datasets. Note that the matrix contains multiple groups of regions (in this case, one for each chromosome used). $ plot...
computeMatrix.rst correctGCBias.rst multiBamSummary.rst multiBigwigSummary.rst plotCorrelation.rst plotCoverage.rst plotFingerprint.rst plotHeatmap.rst plotPCA.rst plotProfile.rst about.rst advanced_features.rst api.rst changelog.rst example_api_tutorial.rst example_gallery.rst example_step_by_step.rs...
Usage examples .. argparse:: :ref: deeptools.plotHeatmap.parse_arguments :prog: plotHeatmap Details plotHeatmap does not change the values that computeMatrix calculated, it simply translates them into heatmaps and summary plots. It offers a large variety of parameters to explore various visualiz...