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      "page": "keep_abundant-SummarizedExperiment-method",
      "title": "keep_abundant",
      "topics": [
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    {
      "page": "keep_variable-methods",
      "title": "Keep variable transcripts",
      "topics": [
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        "keep_variable,RangedSummarizedExperiment-method",
        "keep_variable,SummarizedExperiment-method"
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    {
      "page": "log10_reverse_trans",
      "title": "Log10 reverse transformation for ggplot2",
      "topics": [
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    },
    {
      "page": "logit_trans",
      "title": "logit scale",
      "topics": [
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    {
      "page": "pivot_sample-methods",
      "title": "Extract sample-wise information",
      "topics": [
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        "pivot_sample,SummarizedExperiment-method"
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      "title": "Extract transcript-wise information",
      "topics": [
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        "pivot_transcript,RangedSummarizedExperiment-method",
        "pivot_transcript,SummarizedExperiment-method"
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    {
      "page": "quantile_normalise_abundance-methods",
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      "topics": [
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        "quantile_normalise_abundance,SummarizedExperiment-method"
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      "title": "Dimension reduction of the transcript abundance data",
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        "reduce_dimensions,SummarizedExperiment-method"
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        "remove_redundancy,RangedSummarizedExperiment-method",
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      "title": "Rotate two dimensions (e.g., principal components) of an arbitrary angle",
      "topics": [
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      "page": "scale_abundance-methods",
      "title": "Scale the counts of transcripts/genes",
      "topics": [
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        "scale_abundance,RangedSummarizedExperiment-method",
        "scale_abundance,SummarizedExperiment-method"
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    {
      "page": "test_differential_abundance-methods",
      "title": "Perform differential transcription testing using edgeR quasi-likelihood (QLT), edgeR likelihood-ratio (LR), limma-voom, limma-voom-with-quality-weights or DESeq2",
      "topics": [
        "test_differential_abundance",
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      "title": "Perform differential expression testing using edgeR quasi-likelihood (QLT), edgeR likelihood-ratio (LR), limma-voom, limma-voom-with-quality-weights or DESeq2",
      "topics": [
        "test_differential_expression",
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      "title": "analyse gene over-representation with GSEA",
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      "title": "analyse gene rank with GSEA",
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        "Abundance Normalization Functions",
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        "Abundance Filtering",
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      "created": "2019-09-11 09:21:30",
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