All functions |
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UMI4C class methods |
UMI4C-class |
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UMI4Cats object to DDS object. |
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UMI4Cats: A package for analyzing UMI-4C chromatin contact data |
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Add grouping of UMI-4C samples |
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Add stepping for plotting genes |
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UMI4C alignment |
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Adaptative smoothing of normalized trend |
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Create Domainogram |
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Call significant interactions |
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Combine UMI4C fragments |
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UMI4C Contacts Processing |
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UMI counting |
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Create gene annotation object |
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Create stats table |
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Darken colors |
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DDS object to UMI4Cats object. |
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Demultiplex FASTQ files using fastq-multx |
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Differential UMI4C contacts using DESeq2 Wald Test |
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Digest reference genome |
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Get BiocFileCache object |
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Summarize BAM file |
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Align split fastq file |
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Count UMIs for a given bam file. |
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Prepar fastq files at a given barcode. |
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Split fastq files at a given restriction site. |
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Monotone smoothing of the VST counts |
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Download UMI4Cats example datasets |
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Contacs with CIITA promoter |
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Differential UMI4C contacts using Fisher's Exact test |
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Format plots for UMI4C |
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Get geometric mean of given coordinates |
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Get default colors |
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Get factors fro plotting |
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Get normalization matrix |
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Get significant interactions from a GRangesList |
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Get viewpoint coordinates |
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Group UMI4C samples |
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Make windows merging restriction fragments |
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Differential UMI4C contacts using DESeq2 Wald Test |
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Plot differential contacts |
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Plot domainogram |
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Plot genes |
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Plot interactions |
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Plot Interactions UMI4C |
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Plot adaptative smoothen trend |
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Plot UMI4C data |
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Prepare UMI4C data |
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Monotone smoothing of the DDS object VST counts |
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Split UMI4C reads |
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Statistics UMI4C |
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Theme |
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Theme Y blank |
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Theme X blank |
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Theme Y blank |
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Variance stabilizing transformation |
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DESeq2 Wald test for differential contacts |
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Z-score calculation using residuals of trend and fit UMI4C counts |