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Add a readthedocs page for plotEnrichment, fixes #408
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@dpryan79
dpryan79 committed Aug 23, 2016
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66 changes: 35 additions & 31 deletions docs/content/list_of_tools.rst
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Expand Up @@ -14,37 +14,39 @@ The tools
.. contents::
:local:

+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
| tool | type | input files | main output file(s) | application |
+================================+==================+===================================+============================================+===================================================================================+
|:doc:`tools/multiBamSummary` | data integration | 2 or more BAM | interval-based table of values | perform cross-sample analyses of read counts --> plotCorrelation, plotPCA |
+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/multiBigwigSummary` | data integration | 2 or more bigWig | interval-based table of values | perform cross-sample analyses of genome-wide scores --> plotCorrelation, plotPCA |
+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/plotCorrelation` | visualization | bam/multiBigwigSummary output | clustered heatmap | visualize the Pearson/Spearman correlation |
+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/plotPCA` | visualization | bam/multiBigwigSummary output | 2 PCA plots | visualize the principal component analysis |
+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/plotFingerprint` | QC | 2 BAM | 1 diagnostic plot | assess enrichment strength of a ChIP sample |
+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/computeGCBias` | QC | 1 BAM | 2 diagnostic plots | calculate the exp. and obs. GC distribution of reads |
+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/correctGCBias` | QC | 1 BAM, output from computeGCbias | 1 GC-corrected BAM | obtain a BAM file with reads distributed according to the genome’s GC content |
+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/bamCoverage` | normalization | BAM | bedGraph or bigWig | obtain the normalized read coverage of a single BAM file |
+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/bamCompare` | normalization | 2 BAM | bedGraph or bigWig | normalize 2 files to each other (e.g. log2ratio, difference) |
+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/computeMatrix` | data integration | 1 or more bigWig, 1 or more BED | zipped file for plotHeatmap or plotProfile | compute the values needed for heatmaps and summary plots |
+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/plotHeatmap` | visualization | computeMatrix output | heatmap of read coverages | visualize the read coverages for genomic regions |
+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/plotProfile` | visualization | computeMatrix output | summary plot (“meta-profile”) | visualize the average read coverages over a group of genomic regions |
+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/plotCoverage` | visualization | 1 or more bam | 2 diagnostic plots | visualize the average read coverages over sampled genomic positions |
+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/bamPEFragmentSize` | information | 1 BAM | text with paired-end fragment length | obtain the average fragment length from paired ends |
+--------------------------------+------------------+-----------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
| tool | type | input files | main output file(s) | application |
+================================+==================+=====================================+============================================+===================================================================================+
|:doc:`tools/multiBamSummary` | data integration | 2 or more BAM | interval-based table of values | perform cross-sample analyses of read counts --> plotCorrelation, plotPCA |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/multiBigwigSummary` | data integration | 2 or more bigWig | interval-based table of values | perform cross-sample analyses of genome-wide scores --> plotCorrelation, plotPCA |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/plotCorrelation` | visualization | bam/multiBigwigSummary output | clustered heatmap | visualize the Pearson/Spearman correlation |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/plotPCA` | visualization | bam/multiBigwigSummary output | 2 PCA plots | visualize the principal component analysis |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/plotFingerprint` | QC | 2 BAM | 1 diagnostic plot | assess enrichment strength of a ChIP sample |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/computeGCBias` | QC | 1 BAM | 2 diagnostic plots | calculate the exp. and obs. GC distribution of reads |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/correctGCBias` | QC | 1 BAM, output from computeGCbias | 1 GC-corrected BAM | obtain a BAM file with reads distributed according to the genome’s GC content |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/bamCoverage` | normalization | BAM | bedGraph or bigWig | obtain the normalized read coverage of a single BAM file |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/bamCompare` | normalization | 2 BAM | bedGraph or bigWig | normalize 2 files to each other (e.g. log2ratio, difference) |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/computeMatrix` | data integration | 1 or more bigWig, 1 or more BED | zipped file for plotHeatmap or plotProfile | compute the values needed for heatmaps and summary plots |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/plotHeatmap` | visualization | computeMatrix output | heatmap of read coverages | visualize the read coverages for genomic regions |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/plotProfile` | visualization | computeMatrix output | summary plot (“meta-profile”) | visualize the average read coverages over a group of genomic regions |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/plotCoverage` | visualization | 1 or more BAM | 2 diagnostic plots | visualize the average read coverages over sampled genomic positions |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/bamPEFragmentSize` | information | 1 BAM | text with paired-end fragment length | obtain the average fragment length from paired ends |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`tools/plotEnrichment` | visualization | 1 or more BAM and 1 or more BED/GTF | A diagnostic plot | plots the fraction of alignments overlapping the given features |
+--------------------------------+------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+

General principles
^^^^^^^^^^^^^^^^^^
Expand Down Expand Up @@ -144,3 +146,5 @@ Heatmaps and summary plots
""""""""""""""""""""""""
:doc:`tools/plotProfile`
""""""""""""""""""""""""
:doc:`tools/plotEnrichment`
"""""""""""""""""""""""""""

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