Resources - meyermicrobiolab/Meyer_Lab_Resources GitHub Wiki
- HiPer Gator Cheat Sheet
- GitHub Cheat Sheet/Resources
- Trainings and Quick Start Videos for help with HiPer Gator
- Submitting Sequences to NCBI through FTP
- Julie's command line cheatsheet
- Using command line to change the name of your files in HiPerGator.
- Bioinformatics Workbook - covers many areas
- Happy Belly Bioinformatics (resource for beginners)
- Five things I wish I knew when I started bioinformatics
- How to Learn Coding as a Biologist
- swirl (learn R)
- R-Studio Bootcamp (short and sweet R-studio bootcamp worksheet for running R-studio)
- Cookbook for R (book - graphics with ggplot2)
- Fundamentals of Data Visualization (book - making the best figures)
- R for Data Science (book - using the "tidyverse")
- cowplot (for multi-panel ggplot2 figures)
- patchwork (also for multi-panel ggplot2 figures)
- RStudio Cheatsheets
- Julie's R tricks
- Help, I've got way too many amplicon sequences to run on my laptop run an R script on hipergator
- Riffomonas on YouTube
- Importing Many Data Files Simultaneously
- Introduction to R for Biology & Ecology, undergraduate level
- JM's go-to starting point: cookbook for R/a colorblind-friendly palette
- R pkg with more colorblind-friendly palettes - up to 9 colors
- colorBlindness Guide
- What to consider when visualizing data for colorblind readers
- Coloring for Colorblindness - put in your own palette to see how others can see them
- R Color Palettes: National Park Posters version
- R Color Palettes: Paletteer
- R Color Palettes: Woods Hole
- Mapping continuous variables to phylogenetic trees
- R Color Palettes and Point Shapes (JM's tips---older, but it shows how to create a custom palette that you can use with a colorblind-friendly palette)
- From Data to Viz - gallery of visualizations and the code to make them, with suggestions for the type of data you have
- The R Graph Gallery
- Beyond Bar and Line Graphs
- IAN symbol library - free academic resource for icons related to ecology, landscapes, organisms
- free icons - NIH bioart
- free icons - bioicons
- free icons - healthicons
- free icons - reactome
- Making a Gantt Chart
- Making a Bubbleplot
- ggenes - plot gene clusters with customized gene lengths, colors
- How To: Cut-Adapt for 16S Analysis
- Installing ALDEx, CoDaSeq, dada2, phyloseq with devtools and BiocManager
- Sorting Samples by Metadata (get rid of default alphabetical-order)
- Subset samples in a phyloseq object by metadata
- Get abundant Taxa
- Indicator Species analysis with indicspecies R pkg
- DADA2 Tutorial
- Phyloseq Tutorials
- Intro to multivariate data analysis using vegan
- Phyloseq Object to LEfSe
- ANCOM function - must be run first before applying to data
- MicroViz - microbiome data analysis
- Phinch
- R to Qiime2 for ANCOM
- Qiime2 Pipeline
- minimalR: tutorials from Schloss lab on making common microbiome figures in R
- LEfSe on Galaxy
- Dirichlet Multinomial
- Time Series Analysis
- Corncob tutorial
- Microbiome R pkg
- Differential Abundance - Options & Code
- How to multiQC - summarize fastQC files
- Basic Genomics Workflow
- Basic Metagenomics Workflow
- Basic Metatranscriptomics Workflow
- Series of youtube tutorials for using IMG resources
- IMG Comparative Genomics/Metagenomics Workshop 2023 Resources
- Kostas lab tools - MiGA, ANI, non-pareil
- MiGA online (id and check completeness of MAGs)
- antiSMASH
- antiSMASH Results Webscraper
- BiG-SCAPE
- Meren lab's Intro to Microbial 'Omics
- workflow for metagenomes in anvi'o
- anvi'o metagenomics tutorial
- anvi'o - all programs/scripts
- Anvi'o Pangenomic Workflow
- BioBakery - Huttenhower lab
- Roary and Phandango
- clinker - gene cluster visualization tool
- Genome Taxonomy Database aka GTDB
- Writing tips
- How to Write a Response to Reviewers
- Recipe for a Proposal
- Outreach Ideas
- Professional Development tools
- Work-life balance / self-care
- 9 tips for successful postdoc
- DiversifyMicrobiology - self-nominate (with PhD), search for seminar speakers, etc. includes links to other collections of diverse speakers too
- Strategies and support for Black, Indigenous, and people of colour in ecology and evolutionary biology (in Nature journal)
- Examples of successful job application packets: Industry, PUI, R1
- PhD Roadmap with UF grad student resources
- Navigating Grad School: A Professional Development Workbook
- Search UF dissertations to see examples
- What to bring to a meeting with your advisor
- Preparing for Qualifying Exams
- Preparing to graduate: UF Grad School deadlines for dissertation