# MarkList **Repository Path**: ShixiangWang/MarkList ## Basic Information - **Project Name**: MarkList - **Description**: No description available - **Primary Language**: Unknown - **License**: GPL-3.0 - **Default Branch**: main - **Homepage**: None - **GVP Project**: No ## Statistics - **Stars**: 0 - **Forks**: 0 - **Created**: 2021-12-27 - **Last Updated**: 2022-04-14 ## Categories & Tags **Categories**: Uncategorized **Tags**: None ## README # Shixiang's Mark List This repo is a collection of web resources along my study journey. It is similar to the repo [getting-started-with-genomics-tools-and-resources](https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources) of [Ming Tang](https://github.com/crazyhottommy) but here for my own. I would be appreciated if you can give me feedback if you find something is uncorrect/outdated/missing. ************************* ## Recommended list - [crazyhottommy/getting-started-with-genomics-tools-and-resources: Unix, R and python tools for genomics and data science](https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources) - [Mikoto10032/DeepLearning: 深度学习入门教程, 优秀文章, Deep Learning Tutorial](https://github.com/Mikoto10032/DeepLearning) - [Big Book of R](https://www.bigbookofr.com/index.html) ## Awesome list - [awesome-R: A curated list of awesome R packages, frameworks and software](https://github.com/qinwf/awesome-R) - [vinta/awesome-python: A curated list of awesome Python frameworks, libraries, software and resources](https://github.com/vinta/awesome-python) - [grabear/awesome-rshiny: An awesome R-shiny list!](https://github.com/grabear/awesome-rshiny) - [nanxstats/awesome-shiny-extensions: Awesome R packages that offer extended UI or server components for the R web framework Shiny](https://github.com/nanxstats/awesome-shiny-extensions) - [IndrajeetPatil/awesome-r-pkgtools](https://github.com/IndrajeetPatil/awesome-r-pkgtools) - [ropensci-archive/PackageDevelopment](https://github.com/ropensci-archive/PackageDevelopment) ## Books/Materials ### Bioinformatics tutorial - [montilab/BS831](https://montilab.github.io/BS831/) https://github.com/montilab/BS831 ### Programming ### Data science - [Modern R with the tidyverse](https://b-rodrigues.github.io/modern_R/) ## Consoles - [randy3k/radian: A 21 century R console](https://github.com/randy3k/radian) - [IPython: Productive Interactive Computing](https://github.com/ipython/ipython) - [ptpython: A better Python REPL](https://github.com/prompt-toolkit/ptpython/) - [RStudio](https://www.rstudio.com/) - [VS Code](https://code.visualstudio.com/) - [Idea](https://www.jetbrains.com/idea/) - [Jupyter](https://jupyter.org/) ## Data Science ### Toolkits (multifunctionality) - [tidyverse](https://github.com/tidyverse/) - [data.table](https://github.com/Rdatatable/data.table) ### Data import and export ### Data cleaning - [sfirke/janitor: simple tools for data cleaning in R](https://github.com/sfirke/janitor) ### Visualization ### Writing, Reporting and Sharing - [tufte: a style that Edward Tufte uses in his books and handouts](https://rstudio.github.io/tufte/) ### Omics - [lawremi/ggbio: Grid and ggplot2 based visualization for biological data](https://github.com/lawremi/ggbio) - ## Development ### GitHub actions - [r-lib/gh: Minimalistic GitHub API client in R](https://github.com/r-lib/gh) - [r-lib/ghactions: GitHub actions for R and accompanying R package](https://github.com/r-lib/ghactions) ### CLI/GUI - [spf13/cobra-cli: Cobra CLI tool to generate applications and commands](https://github.com/spf13/cobra-cli) ### R #### Materials - [R Packages](https://r-pkgs.org/) - Book - [Writing R Packages](http://www.danieldsjoberg.com/writing-R-packages/) - Slides - [R package submission](https://cran.r-project.org/submit.html) - [Bioconductor - Developers](https://www.bioconductor.org/developers/) - [Bioconductor - Using Bioc Devel](https://www.bioconductor.org/developers/how-to/useDevel/) - [Workshop: Building a Bioconductor Package • BuildingBioCPackage - Bioc2020RCWL](https://saskiafreytag.github.io/making_bioconductor_pkg/articles/workshop.html) #### Data science - [rstudio: Pin, Discover and Share Resources](https://github.com/rstudio/pins) - [lockedata/pRojects: R Package 📦 for making projects for various R activities](https://github.com/lockedata/pRojects) - [rich-iannone/pointblank: Data validation and organization of metadata for data frames and database tables](https://github.com/rich-iannone/pointblank) - [hafen/rminiconda: Install and maintain isolated miniconda Python installations from R](https://github.com/hafen/rminiconda) - [klmr/box: Write reusable, composable and modular R code](https://github.com/klmr/box) - [r-lib/zeallot: Variable assignment with zeal! (or multiple, unpacking, and destructuring assignment in R)](https://github.com/r-lib/zeallot) - [Merck/pkglite: Compact Package Representations](https://github.com/Merck/pkglite) - [ThinkR-open/attachment](https://github.com/ThinkR-open/attachment) - [fstpackage/fst: Lightning Fast Serialization of Data Frames for R](https://github.com/fstpackage/fst) #### Package Scaffolds: - [r-lib/devtools: Tools to make an R developer's life easier](https://github.com/r-lib/devtools) - [r-lib/usethis: automates repetitive tasks that arise during project setup and development, both for R packages and non-package projects](https://github.com/r-lib/usethis) - [lcolladotor/biocthis: Automate package and project setup for Bioconductor packages](https://github.com/lcolladotor/biocthis) - [workflowr/workflowr: Organize your project into a research website](https://github.com/workflowr/workflowr) Developments: - [hadley/assertthat: User friendly assertions for R](https://github.com/hadley/assertthat) - [r-lib/callr: Call R from R](https://github.com/r-lib/callr) - [r-lib/crayon: R package for colored terminal output](https://github.com/r-lib/crayon#readme) - [r-lib/fs: Provide cross platform file operations based on libuv](https://github.com/r-lib/fs) - [tidyverse/glue: Glue strings to data in R. Small, fast, dependency free interpreted string literals](https://github.com/tidyverse/glue) - [hadley/lazyeval: Lazy evaluation: an alternative to non-standard evaluation (NSE) for R](https://github.com/hadley/lazyeval) - [r-lib/ps: R package to query, list, manipulate system processes](https://github.com/r-lib/ps) - [r-lib/R6: Encapsulated object-oriented programming for R](https://github.com/r-lib/R6) - [r-lib/rappdirs: Find OS-specific directories to store data, caches, and logs. A port of python's AppDirs](https://github.com/r-lib/rappdirs) - [r-lib/sloop: interactively explore and understand object oriented programming in R, particularly with S3](https://github.com/r-lib/sloop) - [tidyverse/tidyselect: A backend for selecting functions of the tidyverse](https://github.com/tidyverse/tidyselect) - [Q-language/chk: An R package for developers to check user-supplied function arguments](https://github.com/Q-language/chk) - [wch/staticimports: Statically import R functions into packages and projects](https://github.com/wch/staticimports) logging: - [s-fleck/lgr: A fully featured logging framework for R](https://s-fleck.github.io/lgr/articles/lgr.html) - [daroczig/logger: A lightweight, modern and flexible, log4j and futile.logger inspired logging utility for R](https://github.com/daroczig/logger/) - [devOpifex/err: Error & warning handling for R inspired by go](https://github.com/devOpifex/err) - [johnmyleswhite/log4r: A log4j derivative for R](https://github.com/johnmyleswhite/log4r) - [krlmlr/plogr: R bindings for the plog C++ logging library](https://github.com/krlmlr/plogr#readme) - [r-lib/sessioninfo: Print Session Information](https://github.com/r-lib/sessioninfo) #### CLI - [jokergoo/GetoptLong: Parse command-line arguments and simple variable interpolation](https://github.com/jokergoo/GetoptLong) - [gaborcsardi/ask: Friendly CLI interaction in R](https://github.com/gaborcsardi/ask) - [r-lib/cli: Tools for making beautiful & useful command line interfaces](https://github.com/r-lib/cli) - [devOpifex/cmd: Code generator to produce CLI for R packages](https://github.com/devOpifex/cmd) - [docopt/docopt.R: Command-line interface description language for R (http://docopt.org)](https://github.com/docopt/docopt.R) #### RStudio plugins - [gadenbuie/shrtcts: Make Anything an RStudio Shortcut](https://github.com/gadenbuie/shrtcts) #### Docs - [formatR - Format R code automatically - Yihui Xie | 谢益辉](https://yihui.name/formatR) - [jimhester/lintr: Static Code Analysis for R](https://github.com/jimhester/lintr) - [hafen/packagedocs: simple generation and automated deployment of nice-looking online R package documentation](https://github.com/hafen/packagedocs) - [r-lib/pkgdown: Generate static html documentation for an R package](https://github.com/r-lib/pkgdown) - [cynkra/fledge: Wings for your R packages: Streamline the process of versioning R packages and updating NEWS](https://github.com/cynkra/fledge) #### Check - [r-lib/testthat: An R package to make testing](https://github.com/r-lib/testthat) - [mikldk/roxytest: Inline testthat tests with roxygen2](https://github.com/mikldk/roxytest) - [markvanderloo/tinytest: A lightweight, no-dependency, but full-featured package for unit testing in R](https://github.com/markvanderloo/tinytest) - [ropenscilabs/cchecks: R client for the cranchecks.info API](https://github.com/ropenscilabs/cchecks) - [r-lib/debugme: Easy and efficient debugging for R packages](https://github.com/r-lib/debugme) - [moodymudskipper/flow: View and Browse Code Using Flow Diagrams](https://github.com/moodymudskipper/flow) - [r-lib/rcmdcheck: Run R CMD check from R and collect the results](https://github.com/r-lib/rcmdcheck) - #### Performance Estimation: - [wlandau/proffer: Profile R code with pprof](https://github.com/wlandau/proffer) Optimization: - [eddelbuettel/rcppexamples: Examples of using Rcpp to interface R and C++](https://github.com/eddelbuettel/rcppexamples) - [RcppCore/RcppParallel](https://github.com/RcppCore/RcppParallel) - [DavisVaughan/cbuild: Tools to Make Developing R Packages Interfacing with C Easier](https://github.com/DavisVaughan/cbuild) - [nchern/go-R: Go bindings for R language](https://github.com/nchern/go-R) - [glycerine/rmq: R package providing msgpack and websockets; demonstrates how to utilize Go libraries from R](https://github.com/glycerine/rmq) - [moodymudskipper/refactor: Tools for Refactoring Code](https://github.com/moodymudskipper/refactor) Parallelism: - [HenrikBengtsson/future: Unified Parallel and Distributed Processing in R for Everyone](https://github.com/HenrikBengtsson/future) - [RevolutionAnalytics/foreach: R package to provide foreach looping construct](https://github.com/RevolutionAnalytics/foreach) - [HenrikBengtsson/doFuture: R package: doFuture - A Universal Foreach Parallel Adaptor using the Future API of the 'future' Package](https://github.com/HenrikBengtsson/doFuture) - [doMC: Foreach Parallel Adaptor for 'parallel'](https://github.com/cran/doMC) - [doParallel: Foreach Parallel Adaptor for the 'parallel' Package](https://github.com/cran/doParallel) - [DavisVaughan/furrr: Apply Mapping Functions in Parallel using Futures](https://github.com/DavisVaughan/furrr) - ### Python #### Materials - [Packaging Python Projects — Python Packaging User Guide](https://packaging.python.org/tutorials/packaging-projects/#classifiers) - [Building Beautiful Command Line Interfaces with Python](https://codeburst.io/building-beautiful-command-line-interfaces-with-python-26c7e1bb54df) - [Twine’s documentation](https://twine.readthedocs.io/en/latest/) - [Python 代码调试技巧](https://www.ibm.com/developerworks/cn/linux/l-cn-pythondebugger/) - [IPython 交互式调试器 - 鸣一的专栏 - CSDN博客](https://blog.csdn.net/mdming412/article/details/52334525) - [Sphinx Themes — Write the Docs](https://www.writethedocs.org/guide/tools/sphinx-themes/) - [kyclark/tiny_python_projects: Code for Tiny Python Projects (Manning, 2020, ISBN 1617297518). Learning Python through test-driven development of games and puzzles](https://github.com/kyclark/tiny_python_projects) - [kyclark/biofx_python: Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)](https://github.com/kyclark/biofx_python) #### Tools - [kyclark/new.py: Python program to write new Python programs](https://github.com/kyclark/new.py) - [python/mypy: Optional static typing for Python 3 and 2 (PEP 484)](https://github.com/python/mypy) - [argparse — Parser for command-line options, arguments and sub-commands](https://docs.python.org/3/library/argparse.html) - [json — JSON encoder and decoder](https://docs.python.org/3/library/json.html#module-json) - [Typer: build great CLIs. Easy to code. Based on Python type hints](https://typer.tiangolo.com/) - [flit: A simple packaging tool for simple packages](https://pypi.org/project/flit/) - [pallets/click: Python composable command line interface toolkit](https://github.com/pallets/click) - [fastai/nbdev: Create delightful python projects using Jupyter Notebooks](https://github.com/fastai/nbdev/) - [audreyr/cookiecutter: A command-line utility that creates projects from cookiecutters (project templates). E.g. Python package projects, jQuery plugin projects](https://github.com/audreyr/cookiecutter) - [audreyr/cookiecutter-pypackage: Cookiecutter template for a Python package](https://github.com/audreyr/cookiecutter-pypackage) - [pyscaffold/pyscaffold: 🛠 Python project template generator with batteries included](https://github.com/pyscaffold/pyscaffold) - [dephell/dephell: Python project management. Manage packages: convert between formats, lock, install, resolve, isolate, test, build graph, show outdated, audit. Manage venvs, build package, bump version](https://github.com/dephell/dephell) - [PyInstaller: freezes (packages) Python applications into stand-alone executables, under Windows, GNU/Linux, Mac OS X, FreeBSD, Solaris and AIX](http://www.pyinstaller.org/) - [Pipenv: Python Dev Workflow for Humans](https://pipenv.readthedocs.io/en/latest/) - [Delgan/loguru: Python logging made (stupidly) simple](https://github.com/Delgan/loguru) - [cool-RR/PySnooper: Never use print for debugging again](https://github.com/cool-RR/pysnooper) - [Making a PyPI-friendly README — Python Packaging User Guide](https://packaging.python.org/guides/making-a-pypi-friendly-readme/) - [sphinx.ext.napoleon – Support for NumPy and Google style](http://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html) - [mkdocs/mkdocs: Project documentation with Markdown](https://github.com/mkdocs/mkdocs) - [beeware/toga: A Python native, OS native GUI toolkit](https://github.com/beeware/toga) - [willmcgugan/rich: Rich is a Python library for rich text and beautiful formatting in the terminal](https://github.com/willmcgugan/rich) - [joerick/pyinstrument: 🚴 Call stack profiler for Python. Shows you why your code is slow!](https://github.com/joerick/pyinstrument) - [tiangolo/fastapi: FastAPI framework, high performance, easy to learn, fast to code, ready for production](https://github.com/tiangolo/fastapi) - [tqdm/tqdm: A Fast, Extensible Progress Bar for Python and CLI](https://github.com/tqdm/tqdm) - [prompt-toolkit/python-prompt-toolkit: Library for building powerful interactive command line applications in Python](https://github.com/prompt-toolkit/python-prompt-toolkit) - [ActiveState/appdirs: A small Python module for determining appropriate platform-specific dirs, e.g. a "user data dir".](https://github.com/ActiveState/appdirs) ### Web apps #### Materials - [中文教程：用R构建Shiny应用程序](http://yanping.me/shiny-tutorial/#welcome) - [storybookjs/storybook: 📓 The UI component explorer. Develop, document, & test for React, Vue, Angular, Ember, Web Components, & more!](https://github.com/storybookjs/storybook) - [microsoft/Web-Dev-For-Beginners: 24 Lessons, 12 Weeks, Get Started as a Web Developer](https://github.com/microsoft/Web-Dev-For-Beginners) - [davidruvolo51/shinyAppTutorials: a collection of shiny app demonstrations](https://github.com/davidruvolo51/shinyAppTutorials) - [Argon Design System - Free Design System for Bootstrap 4](https://demos.creative-tim.com/argon-design-system/) - [shinyapps.io user guide](https://docs.rstudio.com/shinyapps.io/index.html) - [jienagu/Shiny_Full_Flow: This app demonstrates the basic work flow from data entry to dynamic report.](https://github.com/jienagu/Shiny_Full_Flow) - [smee.io | Webhook payload delivery service](https://smee.io/) - [dreamRs/fresh: Fresh shiny themes](https://github.com/dreamRs/fresh) - [ericrayanderson/shinymaterial](https://github.com/ericrayanderson/shinymaterial) - [ThinkR-open/shinysnippets: A series of shiny related RStudio Snippets](https://github.com/ThinkR-open/shinysnippets) - [r4fun/icongram: Icongram for R](https://github.com/r4fun/icongram) - [Icons | Font Awesome](https://fontawesome.com/icons?d=gallery) #### Tools - [ropensci/plotly: An interactive graphing library for R](https://github.com/ropensci/plotly) - [JohnCoene/echarts4r: 🐳 ECharts 4 for R](https://github.com/JohnCoene/echarts4r) - [JohnCoene/g2r: 📈Grammar of graphics for interactive visualisations](https://github.com/JohnCoene/g2r) - [Creating APIs in R with Plumber](https://www.rplumber.io/docs/) - [Shiny: Easy interactive web applications with R](https://github.com/rstudio/shiny) - [plotly/dash: Analytical Web Apps for Python & R. No JavaScript Required](https://github.com/plotly/dash/) - [XD-DENG/ECharts2Shiny: To insert interactive charts from ECharts into R Shiny applications (在R Shiny app中插入ECharts可交互图形)](https://github.com/XD-DENG/ECharts2Shiny) - [RinteRface/shinybulma: 🌐 Bulma.io for Shiny](https://github.com/RinteRface/shinybulma) - [jcrodriguez1989/shinyParallel: Run Shiny applications in a multi-session mode](https://github.com/jcrodriguez1989/shinyParallel) - [Custom Inputs Widgets for Shiny • shinyWidgets](https://dreamrs.github.io/shinyWidgets/) - [JohnCoene/waiter: 🕰️ Loading screens for Shiny](https://github.com/JohnCoene/waiter) - [dm3ll3n/ShinyStudio: a curated, out-of-the-box instance of ShinyProxy that includes RStudio, VS Code, NGINX, InfluxDB to offer a full-featured, easily reproducible, multi-user development environment.](https://github.com/dm3ll3n/ShinyStudio) - [plotly/dash-bio: Open-source bioinformatics components for Dash](https://github.com/plotly/dash-bio) - [great-northern-diver/loon: A Toolkit for Interactive Statistical Data Visualization](https://github.com/great-northern-diver/loon) - [RinteRface/bs4Dash: Bootstrap 4 shinydashboard using AdminLTE3](https://github.com/RinteRface/bs4Dash) - [ThinkR-open/golem: A Framework for Building Robust Shiny Apps](https://github.com/ThinkR-open/golem) - [ColinFay/glouton: 'JS-cookies' in Shiny](https://github.com/ColinFay/glouton) - [moj-analytical-services/shinyGovstyle](https://github.com/moj-analytical-services/shinyGovstyle) - [daattali/shinyjs: Easily improve the user experience of your Shiny apps in seconds](https://github.com/daattali/shinyjs) - [RinteRface/shinyMobile: shiny API for Framework7 (IOS/android)](https://github.com/RinteRface/shinyMobile) - [JohnCoene/shinytitle: Update Shiny Page Title](https://github.com/JohnCoene/shinytitle) - [rstudio/shinymeta: Record and expose Shiny app logic using metaprogramming](https://github.com/rstudio/shinymeta) - [dreamRs/shinylogs: Logs for Shiny apps](https://github.com/dreamRs/shinylogs) - [MazamaScience/beakr: A Minimalist Web Framework for R](https://github.com/MazamaScience/beakr) - [yonicd/reactor: unit testing for shiny reactivity](https://github.com/yonicd/reactor) - [rstudio/reactlog: Shiny Reactivity Visualizer](https://github.com/rstudio/reactlog) - [feddelegrand7/fabricerin: Create Easily Canvas in Shiny and RMarkdown Documents](https://github.com/feddelegrand7/fabricerin) - [DillonHammill/DataEditR: An Interactive R Package for Viewing, Entering and Editing Data](https://github.com/DillonHammill/DataEditR) - [JohnCoene/linne: 🌊 Write CSS in R](https://github.com/JohnCoene/linne) - [Appsilon/shiny.router: A minimalistic router for your Shiny apps.](https://github.com/Appsilon/shiny.router) - [JohnCoene/cicerone: 🏛️ Give tours of your Shiny apps](https://github.com/JohnCoene/cicerone) - [nameko/nameko: Python framework for building microservices](https://github.com/nameko/nameko) - [daattali/shinyalert: Easily create pretty popup messages (modals) in Shiny](https://github.com/daattali/shinyalert) - [Tychobra/polished: Authentication and Administration for Shiny apps](https://github.com/Tychobra/polished) - [RinteRface/shinydashboardPlus: extensions for shinydashboard](https://github.com/RinteRface/shinydashboardPlus/) - [plotly/dashR: Dash for R - An R interface to the Dash ecosystem for creating analytic web applications](https://github.com/plotly/dashR) - [yonicd/slickR: slick carousel htmlwidget for R](https://github.com/yonicd/slickR) - [dreamRs/datamods: Shiny modules to import data into an application or addin](https://github.com/dreamRs/datamods) - [Elm - delightful language for reliable web applications](https://elm-lang.org/) - [trestletech/shinyAce: Integrating the Ace editor with Shiny.](https://github.com/trestletech/shinyAce) - [rexyai/RestRserve: R web API framework for building high-performance microservices and app backends](https://github.com/rexyai/RestRserve) - [Next.js by Vercel - The React Framework](https://nextjs.org/) - [Unitech/pm2: Node.js Production Process Manager with a built-in Load Balancer.](https://github.com/Unitech/pm2) - [vorakl/TrivialRC: A minimalistic RC system and process manager for containers and applications](https://github.com/vorakl/TrivialRC) - [RinteRface/charpente: Seamlessly design robust 'shiny' extensions](https://github.com/RinteRface/charpente) - [vorakl/TrivialRC: A minimalistic RC system and process manager for containers and applications](https://github.com/vorakl/TrivialRC) ## Polishing - [r-lib/asciicast: Turn R scripts into terminal screencasts](https://github.com/r-lib/asciicast) - [GuangchuangYu/hexSticker: Hexagon sticker in R](https://github.com/GuangchuangYu/hexSticker/) ## Pipeline/Workflow - [jtamames/SqueezeMeta: A complete pipeline for metagenomic analysis](https://github.com/jtamames/SqueezeMeta)