baseCallMetrics | Gather basecalling metrics from a Run (using Run's ConversionStats.xml file). |
basecallQC | The basecallQC object and constructor. |
basecallQC-basecallQC | The basecallQC object and constructor. |
basecallQC-class | The basecallQC object and constructor. |
BCL2FastQparams | The Parameters for BCL2FastQparams object. |
BCL2FastQparams-BCL2FastQparams | The Parameters for BCL2FastQparams object. |
BCL2FastQparams-class | The Parameters for BCL2FastQparams object. |
createBasemasks | Function to create basemasks for basecalling from Illumina samplesheet (for bcl2Fastq versions >= 2.1.7). |
createBCLcommand | Function to create command for Illumina basecalling/demultiplexing using bcl2fastq versions >= 2.1.7. |
demultiplexMetrics | Gather demultiplexing metrics from a Run (using Run's DemultiplexingStats.xml file). |
demuxBarplot | Barplot of Illumina demultiplexing statistics. |
demuxBarplot-method | Barplot of Illumina demultiplexing statistics. |
demuxBarplot.basecallQC | Barplot of Illumina demultiplexing statistics. |
demuxBoxplot | Boxplot of Illumina demultiplexing statistics. |
demuxBoxplot-method | Boxplot of Illumina demultiplexing statistics. |
demuxBoxplot.basecallQC | Boxplot of Illumina demultiplexing statistics. |
indexlengths | Index lengths |
indexlengths,BCL2FastQparams-method, | Index lengths |
indexlengths-method | Index lengths |
indexlengths.bcl2fastqparams | Index lengths |
interOpsReport | Function to parse InterOps files and generate summary reports |
makeFQTable | Generate an HTML table linking to per sample summary fastq QC statistics from ShortRead |
passFilterBar | Barplot of Illumina basecalling statistics for reads passing filter. |
passFilterBar-method | Barplot of Illumina basecalling statistics for reads passing filter. |
passFilterBar.basecallQC | Barplot of Illumina basecalling statistics for reads passing filter. |
passFilterBoxplot | Boxplot of Illumina basecalling statistics for reads passing filter. |
passFilterBoxplot-method | Boxplot of Illumina basecalling statistics for reads passing filter. |
passFilterBoxplot.basecallQC | Boxplot of Illumina basecalling statistics for reads passing filter. |
passFilterTilePlot | Tile plot of Illumina basecalling statistics for reads passing filter. |
passFilterTilePlot-method | Tile plot of Illumina basecalling statistics for reads passing filter. |
passFilterTilePlot.basecallQC | Tile plot of Illumina basecalling statistics for reads passing filter. |
readlengths | Read lengths |
readlengths,BCL2FastQparams-method, | Read lengths |
readlengths-method | Read lengths |
readlengths.bcl2fastqparams | Read lengths |
reportBCL | Generate basecallQC report |
reportBCL-method | Generate basecallQC report |
reportBCL.basecallQC | Generate basecallQC report |
summaryConvStatsTable | Creates an HTML table of per sample summary statistics from basecalling results |
summaryConvStatsTable-method | Creates an HTML table of per sample summary statistics from basecalling results |
summaryConvStatsTable.basecallQC | Creates an HTML table of per sample summary statistics from basecalling results |
summaryDemuxTable | Generate an HTML table of per sample summary demultiplexing statistics |
summaryDemuxTable-method | Generate an HTML table of per sample summary demultiplexing statistics |
summaryDemuxTable.basecallQC | Generate an HTML table of per sample summary demultiplexing statistics |
validateBCLSheet | Illumina sample sheet cleaning and updating for bcl2Fastq versions >= 2.1.7 |