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I would be appreciated if you can give me feedback if you find something is uncorrect/outdated/missing.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