├── .gitignore ├── LICENSE ├── README.md ├── methods_resources.xlsx ├── review_spat_trns_methods.Rmd └── review_spat_trns_methods.html /.gitignore: -------------------------------------------------------------------------------- 1 | # History files 2 | .Rhistory 3 | .Rapp.history 4 | 5 | # Session Data files 6 | .RData 7 | 8 | # User-specific files 9 | .Ruserdata 10 | 11 | # Example code in package build process 12 | *-Ex.R 13 | 14 | # Output files from R CMD build 15 | /*.tar.gz 16 | 17 | # Output files from R CMD check 18 | /*.Rcheck/ 19 | 20 | # RStudio files 21 | .Rproj.user/ 22 | 23 | # produced vignettes 24 | vignettes/*.html 25 | vignettes/*.pdf 26 | 27 | # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 28 | .httr-oauth 29 | 30 | # knitr and R markdown default cache directories 31 | *_cache/ 32 | /cache/ 33 | 34 | # Temporary files created by R markdown 35 | *.utf8.md 36 | *.knit.md 37 | 38 | # R Environment Variables 39 | .Renviron 40 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2021 drieslab 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # awesome-spatial-data-analysis 2 | Awesome list of tools and methods to perform spatial transcriptomic data analysis. 3 | 4 | View all the methods here 5 | -------------------------------------------------------------------------------- /methods_resources.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/drieslab/awesome-spatial-data-analysis/b42254ddd8a7b0b1793f49f17725b886f3ffb6c9/methods_resources.xlsx -------------------------------------------------------------------------------- /review_spat_trns_methods.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "spatial-transcriptomics-methods" 3 | output: html_document 4 | --- 5 | 6 | ```{r setup, include=FALSE} 7 | knitr::opts_chunk$set(echo = FALSE) 8 | library(dplyr);library(readxl); library(kableExtra); library(stringr) 9 | options(knitr.table.format = "html", knitr.kable.NA = '') 10 | ``` 11 | 12 | ```{r} 13 | rawdat <- read_excel("~/Downloads/methods_resources.xlsx") 14 | cdat <- rawdat %>% mutate(Category = Category, `Method Type`= `Method Type`, Year = Year, Name = Name, Title = Title, `Programming Language` = `Programming Language`, Reference = Reference) %>% 15 | select(Category, `Method Type`, Year, Name, Title, `Programming Language`, Reference) 16 | 17 | topiclist <- which(!is.na(cdat$Category)) 18 | 19 | knitr::kable(cdat, align="l", "html", escape=FALSE) %>% 20 | kable_styling(bootstrap_options = c("hover", "striped", "responsive")) %>% 21 | column_spec(1, width="1%") %>% column_spec(2, width="1%") %>% 22 | column_spec(3, width="20%") %>% column_spec(4, width="30%") %>% 23 | column_spec(5, width="30%") 24 | ``` 25 | 26 | --------------------------------------------------------------------------------