# An R package to enable organisation and visualisation of nanopore sequencing data

## Documentation for package ‘poRe’ version 0.16

- DESCRIPTION file.

## Help Pages

copy.runs | Process the MinION run folder and copy fast5 files to appropriate sub folders
coreImagePlot | Code from http://www.phaget4.org/R/image_matrix.html. Plot a matrix as a heatmap.
extract.run.fasta | Extract fasta data from a directory of fast5 files
extract.run.fastq | Extract fastq data from a directory of fast5 files
extractfasta | Extract fasta data from a single fast5 file
extractfastq | Extract fastq data from a single fast5 file
fast52fasta | Extract fasta data from a single fast5 file and write to a file
fast52fastq | Extract fastq data from a single fast5 file and write to a file
get.align | Get the saignment table from a fast5 file
get.events | Extract events from a single fast5 file
get.kmer.events | Join the alignment table and the two events tables
get.model.params | Extract model parameters from a fast5 file
get.models | Extract models from a single fast5 file
get_essential_info | Extract meta data from a single fast5 file
get_fast5_info | Extract meta data from a single fast5 file
get_fasta | Extract fasta data from a single fast5 file as a list
get_fastq | Extract fastq data from a single fast5 file as a list
get_meta_info | Extract meta data from a single fast5 file
map.2dfastq.events | Map position of kmer in the 2D fastq sequence to template and complement events that created it
MINION | Metadata from a very early MinION run at Edinburgh Genomics. From 'read.fast5.info'
MINIONEVENTS | EVents data from a MinION fast5 file
plot.as.squiggle | Plot a theoretical "squiggle" of a vector of numbers representing model means
plot.channel.reads | Barplot of the number of reads per channel
plot.channel.summary | Creates heatmap of the MinION flowcell layout
plot.channel.yield | Barplot of the yield per channel
plot.cumulative.yield | Plot cumulative yield for a MinION run
plot.length.histogram | Plot length histogram for a MinION run
plot.squiggle | Plot a theoretical "squiggle" of events from a MinION nanopore read
pore_rt | Experimental GUI for MinION run monitoring
printfasta | Print fasta data from a single fast5 file to STDOUT
printfastq | Print fastq data from a single fast5 file to STDOUT
read.essential.info | Extract meta data from a directory of fast5 files
read.fast5.info | Extract meta data from a directory of fast5 files
read.meta.info | Extract meta data from a directory of fast5 files
run.summary.stats | Extracts key run stats for a MinION run
show.layout | Show the MinION flowcell layout by channel number
summarise.by.channel | Calculate a load of statistics for a MinION run summarised by channel. Takes the output of 'read.meta.info'