Files in wrightrc/r1001genomes
Access and analyze the 1001 genomes Arabidopsis resequencing dataset

.Rbuildignore
.gitignore
DESCRIPTION
Dockerfile
NAMESPACE
R/Strains_and_Gene_Families.R R/VCF_Utils.R README.md
TIR1AFB2.vcf
ToDo
data/SNPeff_order.RData
data/accessions.RData
data/effect_classes.rds
data/gr.rda
data/strains.RData
inst/extdata/AFB_annotations.csv
inst/extdata/AFB_gene_ids.csv
inst/extdata/Araport11_GFF3_genes_transposons.201606.gff.gz
inst/extdata/geneInfoCache.csv
inst/extdata/strains.rds
inst/shiny-app/AppBibliography.bib
inst/shiny-app/AppReferences.bib
inst/shiny-app/Bibliography.Rmd
inst/shiny-app/Bibliography.html
inst/shiny-app/Bibliography.md
inst/shiny-app/Glossary.html
inst/shiny-app/annotations_template.csv
inst/shiny-app/apa.csl
inst/shiny-app/demo_VCFs.rds
inst/shiny-app/fullVCF.vcf.gz
inst/shiny-app/geneInfoCache.txt
inst/shiny-app/global.R inst/shiny-app/server.R inst/shiny-app/ui.R
inst/shiny-app/www/general.css
inst/shiny-app/www/green_theme.css
inst/shiny-app/www/simple_blue_theme.css
install.R man/Nucleotide_diversity.Rd man/VCFByTranscript.Rd man/VCFList.Rd man/addAccDetails.Rd man/addAlnPosToAnno.Rd man/addSNPsToAlnDF.Rd man/alignCDS.Rd man/chunkAlnDF.Rd man/chunkAnnotation.Rd man/diversityStats.Rd man/geneInfoFromFile.Rd man/geneInfoFromGff.Rd man/geom_str_align.Rd man/getCodingDiv.Rd man/getGeneInfo.Rd man/hello.Rd man/labelBySNPs.Rd man/makeAlnDF.Rd man/makeChunksDF.Rd man/parseEFF.Rd man/plotCodingDiv.Rd man/promoterVariantToString.Rd man/readAnnotationFile.Rd man/run1001genomes.Rd man/variantCounts.Rd
r1001genomes.Rproj
vignettes/Screenshots/App_Initial.PNG
vignettes/Screenshots/Tab_1_Gene_Info_Table.PNG
vignettes/Screenshots/Tab_1_Select_Genes.PNG
vignettes/Screenshots/Tab_2_Plot_Data_Table.PNG
vignettes/Screenshots/Tab_2_Plot_Selection_Box.PNG
vignettes/Screenshots/Tab_2_Select_Gene.PNG
vignettes/Screenshots/Tab_3_Map.PNG
vignettes/Screenshots/Tab_3_Map_Data_Table.PNG
vignettes/Screenshots/Tab_3_Map_w_Layers.PNG
vignettes/Screenshots/Tab_3_Mutation_Select.PNG
vignettes/Screenshots/Tab_3_Select_Genes_and_Filters.PNG
vignettes/apa.csl
vignettes/example.R vignettes/example.Rmd
vignettes/example.html
vignettes/example_cache/html/__packages
vignettes/example_files/figure-html/unnamed-chunk-18-1.png
vignettes/example_files/figure-html/unnamed-chunk-18-2.png
vignettes/example_files/figure-html/unnamed-chunk-22-1.png
vignettes/example_files/figure-html/unnamed-chunk-22-2.png
vignettes/fullVCF.vcf.gz
vignettes/geneInfoCache.txt
vignettes/references.bib
wrightrc/r1001genomes documentation built on Sept. 11, 2018, 1:40 a.m.