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/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_Diversity_Stats.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/Screenshots/Tab_4_Filters.PNG
vignettes/Screenshots/Tab_4_Table.png
vignettes/Screenshots/Tab_5_Full.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
