adapter_content | Creates a sorted from most frequent to least frequent... |
calc_adapter_content | Compute adapter content in reads. This function is only... |
calc_format_score | Calculate score based on Illumina format |
calc_over_rep_seq | Calculate sequece counts for each unique sequence and create... |
dimensions | Extract the number of columns and rows for a FASTQ file using... |
find_format | Gets quality score encoding format from the FASTQ file.... |
GC_content | Calculates GC content percentage for each read in the... |
gc_per_read | Calculate GC nucleotide sequence content per read of the... |
kmer_count | Return kmer count per sequence for the length of kmer desired |
overrep_kmer | Generate overrepresented kmers of length k based on their... |
overrep_reads | Sort all sequences per read by count. |
per_base_quality | Compute the mean, median, and percentiles of quality score... |
per_read_quality | Compute the mean quality score per read. 'per_read_quality' |
plot_adapter_content | Creates a bar plot of the top 5 most present adapter... |
plot_GC_content | Generate mean GC content histogram. |
plot_outliers | Determine how to plot outliers. Heuristic used is whether... |
plot_overrep_kmer | Create a box plot of the log2(observed/expected) ratio across... |
plot_overrep_reads | Plot the top 5 seqeunces |
plot_per_base_quality | Generate a boxplot of the per position quality score. |
plot_per_read_quality | Plot the mean quality score per sequence as a histogram. High... |
plot_read_content | Plot the per position nucleotide content. |
plot_read_length | Plot a histogram of the number of reads with each read... |
qual_score_per_read | Calculate the mean quality score per read of the FASTQ... |
read_base_content | Compute nucleotide content per position for a single base... |
read_content | Compute nucleotide content per position. Wrapper function... |
read_length | Creates a data frame of read lengths and the number of reads... |
run_all | Will run all functions in the qckitfastq suite and save the... |
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