Man pages for wrightrc/r1001genomes
Access and analyze the 1001 genomes Arabidopsis resequencing dataset
| addAccDetails | Add accession metadata to a dataset containing ecotype IDs |
| addAlnPosToAnno | Add alignment positions to an annotation data frame |
| addSNPsToAlnDF | Add SNPs and indels to an alignment data frame |
| alignCDS | Make an alignment of Coding sequences |
| chunkAlnDF | Chunk up an alignment data frame to allow facetting over... |
| chunkAnnotation | Add a chunks column to an annotation data frame |
| diversityStats | calculate nucleotide diversity statsistics for a... |
| geneInfoFromFile | make geneInfo dataframe based on .csv file of tair loci and... |
| geneInfoFromGff | get gene information from .gff file |
| geom_str_align | String alignment geom for plotting XStringSet Alignments |
| getCodingDiv | produce dataframe of unique variants on the coding sequence |
| getGeneInfo | Get gene information |
| labelBySNPs | Label accessions with the variants they contain |
| makeAlnDF | Make an alignment data frame for plotting |
| makeChunksDF | Create a chunks data frame from a chunked alignment data... |
| Nucleotide_diversity | Calculate nucleotide diversity for each position in the... |
| parseEFF | Parse the EFF field of the VCF files from 1001genomes.org |
| plotCodingDiv | Plot nucleotide diversity over the coding sequence by codon |
| promoterVariantToString | make DNAStrings of sequences for each gene of each accession |
| readAnnotationFile | Read an annotation file |
| run1001genomes | Run 1001 genomes browser shiny app |
| variantCounts | counts number of variants in certain affect categories use... |
| VCFByTranscript | download VCF, optionally in tidyVCF format |
| VCFList | download and store several VCFs in a list structure, named by... |
