Man pages for abruyneel/AlleleProfileR
Genome editing strategy agnostic variant identification and profiling tool
| AlleleProfileR | AlleleProfileR |
| AlleleProfileR.alternatereference | Determine the allele name of HDR sequences |
| AlleleProfileR.bam | Load a .bam file as a data.frame |
| AlleleProfileR.batch | Start the analysis pipeline |
| AlleleProfileR.batch.recompute | Recompute summary output files |
| AlleleProfileR.batch.summary | Summary function |
| AlleleProfileR.binreads | Bin reads based on genomic postition with respect to certain... |
| AlleleProfileR.cryptic | Identify cryptic coding sequences |
| AlleleProfileR.determine.variants | Determine the allelic variants for a sample and gene |
| AlleleProfileR.execute | Wrapper execute function for the analysis |
| AlleleProfileR.getreads | Bin reads based on genomic postition with respect to certain... |
| AlleleProfileR.map | Align reads to the reference genome |
| AlleleProfileR.merge | Merge paired-end reads |
| AlleleProfileR.parsecodingframe | Profile the codingframe sequence |
| AlleleProfileR.parseleadseq | Parse the lead sequence in a chimeric pair |
| AlleleProfileR.parsetrailseq | Parse the trailing sequence in a chimeric pair |
| AlleleProfileR.plot | Plotting function |
| AlleleProfileR.plot.alignment | Alignment plot function |
| AlleleProfileR.plot.mutationtypes | Plotting function |
| AlleleProfileR.plot.readdept | Histogram of the read-depth |
| AlleleProfileR.plot.seqlogo | Seqlogo plot function |
| AlleleProfileR.preprocess | Preprocess fastq.gz files |
| AlleleProfileR.qc | QC reads using external software |
| AlleleProfileR.qc.simple | Basic QC function for BAM data.frames |
| AlleleProfileR.read.folders | Read folders for .fastq or .bam files |
| AlleleProfileR.sample.distribution | Allelelic variant distribution summary and plotting function |
| AlleleProfileR.sample.distribution.boolean | Allelelic variant distribution summary and plotting function... |
| AlleleProfileR.setup | Set the configuration parameters for executing an analysis |
| AlleleProfileR.simulate | Simulate paired-end reads from fasta files |
| AlleleProfileR.summary.profiled.alleles | Summary statistics of the profiled alleles |
