align |
Align sequence reads to a reference genome via seed-and-vote |
atgcContent |
Calculate percentages of nucleotides A, T, G and C in a sequencing read datafile |
buildindex |
Build index for a reference genome |
cellCounts |
Map and count single-cell RNA data sets |
detectionCall |
Determine detection p values for each gene in an RNA-seq dataset |
detectionCallAnnotation |
Generate annotation data used for calculating detection p values |
exactSNP |
exactSNP - an accurate and efficient SNP caller |
featureCounts |
featureCounts: a general-purpose read summarization function |
findCommonVariants |
Finding the common variants among all input VCF files |
flattenGTF |
Flatten features provided in a GTF/GFF annotation |
getInBuiltAnnotation |
Retrieve in-built annotations provided by featureCounts function |
processExons |
Obtain chromosomal coordiates of each exon using NCBI annotation |
promoterRegions |
Generate annotation for promoter region of genes |
propmapped |
Calculate the proportion of mapped reads/fragments in SAM/BAM files |
qualityScores |
Extract quality score data in a sequencing read dataset |
removeDupReads |
Remove sequencing reads which are mapped to identical locations |
repair |
Re-order paired-end reads to place reads from the same pair next to each other |
RsubreadUsersGuide |
View Rsubread Users Guide |
sam2bed |
Convert a SAM format file to a BED format file |
scanFasta |
Generate simulated reads from a set of transcripts |
simReads |
Generate simulated reads from a set of transcripts |
subjunc |
Align sequence reads to a reference genome via seed-and-vote |
sublong |
Align long sequence reads to a reference genome via seed-and-vote |
txUnique |
Count number of bases unique to each transcript |