Man pages for wrightrc/r1001genomes
Access and analyze the 1001 genomes Arabidopsis resequencing dataset

addAccDetailsAdd accession metadata to a dataset containing ecotype IDs
addAlnPosToAnnoAdd alignment positions to an annotation data frame
addSNPsToAlnDFAdd SNPs and indels to an alignment data frame
alignCDSMake an alignment of Coding sequences
chunkAlnDFChunk up an alignment data frame to allow facetting over...
chunkAnnotationAdd a chunks column to an annotation data frame
diversityStatscalculate nucleotide diversity statsistics for a...
geneInfoFromFilemake geneInfo dataframe based on .csv file of tair loci and...
geneInfoFromGffget gene information from .gff file
geom_str_alignString alignment geom for plotting XStringSet Alignments
getCodingDivproduce dataframe of unique variants on the coding sequence
getGeneInfoGet gene information
labelBySNPsLabel accessions with the variants they contain
makeAlnDFMake an alignment data frame for plotting
makeChunksDFCreate a chunks data frame from a chunked alignment data...
Nucleotide_diversityCalculate nucleotide diversity for each position in the...
parseEFFParse the EFF field of the VCF files from
plotCodingDivPlot nucleotide diversity over the coding sequence by codon
promoterVariantToStringmake DNAStrings of sequences for each gene of each accession
readAnnotationFileRead an annotation file
run1001genomesRun 1001 genomes browser shiny app
variantCountscounts number of variants in certain affect categories use...
VCFByTranscriptdownload VCF, optionally in tidyVCF format
VCFListdownload and store several VCFs in a list structure, named by...
wrightrc/r1001genomes documentation built on Nov. 10, 2019, 12:45 p.m.