From 047712a59ed839ea334e074ea31a2d3af140ed82 Mon Sep 17 00:00:00 2001 From: Astra Bryant Date: Tue, 21 May 2024 17:24:22 -0700 Subject: [PATCH 1/2] Updating installpackages.R --- installpackages.R | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/installpackages.R b/installpackages.R index 3f36c22..d3b43c8 100644 --- a/installpackages.R +++ b/installpackages.R @@ -14,5 +14,8 @@ if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools") BiocManager::install("biomaRt") +BiocManager::install("Biostrings") +library(cubar) -pacman::p_load(shiny,shinyjs,seqinr,htmltools,shinyWidgets,shinythemes,magrittr,tidyverse,openxlsx,read.gb,tools,DT,ggplot2,markdown) + +pacman::p_load(shiny,shinyjs,seqinr,htmltools,shinyWidgets,shinythemes,magrittr,tidyverse,openxlsx,read.gb,tools,DT,ggplot2,markdown,cubar) From 5b1249dba74f8f7584ef040d3e2900ceb2188059 Mon Sep 17 00:00:00 2001 From: Astra Bryant Date: Tue, 21 May 2024 17:25:16 -0700 Subject: [PATCH 2/2] Fixing spelling mistake --- UI/README/README_Features.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/UI/README/README_Features.md b/UI/README/README_Features.md index 068c198..9e8c2b7 100644 --- a/UI/README/README_Features.md +++ b/UI/README/README_Features.md @@ -18,7 +18,7 @@ For user-provided genes/sequences, this tab reports the fractional GC content, c * highly expressed *B. malayi* genes [(Han *et al*, 2020)](https://www.genetics.org/content/216/4/947) * highly expressed *P. pacificus* genes [(Han *et al*, 2020)](https://www.genetics.org/content/216/4/947) -To analyze transgenes, coding sequences can be provided via a text box. To analyze native genes, stable gene or transcript IDs with prefixes "SSTP," "SRAE," "SPAL," "SVE," "NBR," "Bma," "Ppa," or "WB" can be provided either through direct input via the appropriate textbox, or in bulk as a comma-separated text file. Users may also provide a *C. elegans* gene name, provided it is prefaced with the string "Ce-", or *C. elegans* stable transcript IDs as is. Finally, users may direcly provide coding sequences for analysis, either as a 2-column CSV file listing sequence names and coding sequences, or a FASTA file containing named coding sequences. +To analyze transgenes, coding sequences can be provided via a text box. To analyze native genes, stable gene or transcript IDs with prefixes "SSTP," "SRAE," "SPAL," "SVE," "NBR," "Bma," "Ppa," or "WB" can be provided either through direct input via the appropriate textbox, or in bulk as a comma-separated text file. Users may also provide a *C. elegans* gene name, provided it is prefaced with the string "Ce-", or *C. elegans* stable transcript IDs as is. Finally, users may directly provide coding sequences for analysis, either as a 2-column CSV file listing sequence names and coding sequences, or a FASTA file containing named coding sequences. Users may download an Excel file containing fractional GC content values, codon adaptation indices, and coding sequences for the user-provided genes.