Various notes collected over the years. Please, contribute and get in touch!
- scRNA-seq notes
- Hi-C tools
- Hi-C data
- Cancer notes
- scATAC-seq notes
- Immuno notes
- scHi-C notes
- ChIP-seq notes
- SNP notes
- RNA-seq notes
- Methylation notes
- Machine learning notes
- Statistics notes
- Bioinformatics notes
- R notes
- Programming notes
- Python notes
- Data notes
- MDmisc notes
(this repository)
- Job notes
- Conference notes
- Grants notes
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GitHub Classroom tutorials for teachers and students
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OTTR - GitHub sites and courses for busy people
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RStudio Cloud - shared projects, assignments, private spaces. Guide
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Wilson, Greg. “Ten Quick Tips for Creating an Effective Lesson.” PLoS Computational Biology 15, no. 4 (April 2019) - Guide for effective teaching, learning principles, tips for creating lessons. Define your audience, spread and mix topics, formulate problems, make summaries, appeal to visual and linguistic learning channels, identify and correct learner's mistakes, motivate and avoid demotivation, be inclusive.
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Preprint similarity search by DOI. Paper
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Creating and publishing a scientific masterpiece - JCI Editor at Large Ushma S. Neill provides updated advice on generating a scientific manuscript with maximum impact. 40min.
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How to write a superb literature review - Nature, December 4, 2020
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Illustration: get your research the attention it deserves - Inkscape, Autodraw, SciDraw, Noun Project, and other graphics tools. Nature, September 24 2020
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Lists of format-free journals, journals conforming to Your Paper Your Way (YPYW) initiative, the bioRxiv to journals or peer review services (B2J) initiative
- Writing your first academic paper
- Reading academic papers
- The Leek group guide to genomics papers
- Writing reviews of academic papers
- Advanced Data Science knowledge and skills
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10 ingredients for a successful supervisor/PhD student relationship
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Awesome Leadership and Management - Awesome List of resources on leading people and being a manager. Geared toward tech, but potentially useful to anyone.
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Questions for potential advisors - questions for students/trainees before joining the lab
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1on1-questions Mega list of 1 on 1 meeting questions compiled from a variety to sources
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Rules for good lab environment: promote the well-being of all, allow schedule flexibility, show gratitude, treat all like teammates, foster collaborative environment, adjust to unique needs of everyone, respect official off-work days, acknowledge achievements, accept failure and celebrate success, promote the professional development. Twitter thread
- Maestre, Fernando T. “Ten Simple Rules towards Healthier Research Labs.” PLOS Computational Biology 15, no. 4 (April 11, 2019)
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Code of Conduct - Alex's Lemonade Stand example
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Applicant_note.md - Advice to PhD student/post-doc applicants. Source, Code to extract text
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The PI spectrum, by Jean Fan
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10 ingredients for a successful supervisor/PhD student relationship
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awesome-expectations - Examples of academic labs with explicitly stated expectations of themselves and their mentees in the form of written lab manuals, by Olga Botvinnik
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Advice to graduate students tweet with 11 pieces of advice from Tanentzapf Lab
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Advice to collaborating PIs by Ted Laderas
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great-puzzles - A curated list of great puzzles
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opensheetmusicdisplay - OpenSheetMusicDisplay renders sheet music in MusicXML format in your web browser based on VexFlow. OSMD is brought to you by PhonicScore.com. Website
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brew update && brew upgrade && brew doctor && brew cleanup- Optimizing Homebrew -
jaywcjlove/awesome-mac - Collections of best Mac software.
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awesome-stock-resources - A collection of links for free stock photography, video and Illustration websites
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free-photos - Places to find CC0 photos and the like, by Jenny Bryant. Links to websites
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rembg - Remove images background. Python, Docker.
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awesome-air-quality - An awesome list of air quality resources.
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Preprint similarity search Journal Recommender for biorXiv preprints, by GreeneLab. GitHub
- Nicholson, David N., Vincent Rubinetti, Dongbo Hu, Marvin Thielk, Lawrence E. Hunter, and Casey S. Greene. “Linguistic Analysis of the BioRxiv Preprint Landscape.” Preprint. Bioinformatics, March 4, 2021.
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Which human reference genome to use? - differences between genome assemblies
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Twitter-based Poster Session - instructions for organizing virtual poster session, and the PPT template for making a 4-panel poster that looks good on Twitter. Created by @PhotonicsMeetup
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icd Fast ICD-10 and ICD-9 comorbidities, decoding and validation in R