https://github.com/biogenies/amyloid-database-list
https://github.com/biogenies/amyloid-database-list
aggregation amyloid-fibrils amyloidosis aprs database databases fibrils idps interaction prion prions
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/biogenies/amyloid-database-list
- Owner: BioGenies
- Created: 2024-07-17T10:44:21.000Z (12 months ago)
- Default Branch: main
- Last Pushed: 2024-11-14T15:43:47.000Z (8 months ago)
- Last Synced: 2025-02-11T14:26:21.036Z (5 months ago)
- Topics: aggregation, amyloid-fibrils, amyloidosis, aprs, database, databases, fibrils, idps, interaction, prion, prions
- Language: HTML
- Homepage: http://biogenies.info/amyloid-database-list/
- Size: 3.81 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- Contributing: CONTRIBUTING.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/",
out.width = "100%"
)
```
# The dynamic landscape of amyloid-related databases
For an interactive and browse-able list, please visit: https://biogenies.info/amyloid-database-list/.
```{r, echo=FALSE,message=FALSE,results='asis'}
library(glue)
library(magrittr)
library(dplyr)
library(googlesheets4)
write_entry <- function(x) {
res <- glue("1. {Database}: [publication]({doi})", .envir = x)
if(is.character(unlist(x[["link"]])))
res <- glue(res, "[database]({link})", .sep = "; ", .envir = x)
paste0(res, ".")
}
# dat <- readr::read_csv("data/amyloid_db.csv") %>%
# filter(`Current status` == "Active") %>%
# select("Database", "Focus", "Type of data", "Only amyloids", "Includes experimental conditions", "Usability",
# "Includes structural information", "Identifies APRs", "Data sources and links to other db", "Current status", "Published or last update", "doi", "link")
dat <- read_sheet("https://docs.google.com/spreadsheets/d/14eZvhdwBjI4a9AT7DwS3QbYioYorrzAqu3zgNUZqDSA/edit?usp=sharing",sheet = "database_list", col_types = "c") %>%
select(1:14) %>%
filter(`Current status` == "Active") %>%
select("Database", "Focus", "Type of data", "Only amyloids", "Includes experimental conditions", "Usability",
"Includes structural information", "Identifies APRs", "Current status", "Published or last update", "Data sources and links to other db", "doi", "link")
# cat_df <- data.frame(categories = c("Active", "Non-active"),
# nice_names = c("Active", "Non-active"))
cat_df <- data.frame(categories = c("Experimental", "Prediction", "Experimental and prediction"),
nice_names = c("Only experimental data", "Predictions", "Experimental data and predictions"))
all_tools <- sapply(1L:nrow(cat_df), function(ith_category_id) {
part_dat <- dat %>% filter(`Type of data` == cat_df[ith_category_id, "categories"])
row_order <- order(part_dat[["Database"]])
paste0(paste0("## ", cat_df[ith_category_id, "nice_names"], "\n\n"),
paste0(sapply(row_order, function(ith_row)
write_entry(part_dat[ith_row, ])),
collapse = "\n"), "\n\n\n")
})
links <- gsub(pattern = " ", replacement = "-", x = cat_df[["nice_names"]]) %>%
gsub(pattern = "[()]", replacement = "", x = .) %>%
tolower() %>%
paste0("(#", ., ")")
cat(paste0("- [", cat_df[["nice_names"]], "]", links), "\n\n", sep = "\n")
cat(all_tools, sep = "\n")
```
### About and citation
The database was developed by **BioGenies** team. If you want to get to know us and our projects visit our webpage [BioGenies](https://biogenies.info/).
```{r, echo=FALSE,results='asis'}
cat(readLines("./data/citation.md"), sep = "\n")
```
This project was supported by the **National Science Centre Poland**, SONATA 19 grant [**2023/51/D/NZ7/02847**].
[{width=600}](https://ncn.gov.pl/en)
Open access was funded by **Medical University of Białystok**, [**B.SUB.24.592**].
[{width=100}](https://www.umb.edu.pl/en/index.php)