biocode repository
Contains various links
For Reference:
Color Picking
- colormaps and more colormaps and matplotlib colors
- Named Colors
- xkcd color picker
- Map Colors
- Color Hex Color Palettes
- AI generated paint colors
- Fishualize and palettes
- Seaborn
Biology
- JKX Science comics
- Pedigree Reference and Punnett Squares for Blood Type
- Sequence Variants
- Mouse Resources
- An Excellent Explanation of the Multiple Comparisons Issue by Geoffrey Brent
- A good description of the PhD student experience by Yasha Berchenko-Kogan
Bio Downloads
- Selected downloads from Biological databases
Linestyles and Markers
Advice on Color Picking
Code Quality
- Best Practices
- pylint
- pydocstyle
- Google Python Style Guide
- Google Style Examples
- PyPI release checklist
- What every programmer should know
LaTex
- Overleaf keyboard shortcuts
- https://www.sharelatex.com/learn
- Equations with LaTeX
- Adding references from an external file
- Referring to labels in other documents
- Greek letters
- Cover letter tips
- Awesome CV
- Editing Services
- vim
Statistics
- Allen Downey's ThinkStats2
- Simply Statistics
- A biologist's guide to statistical thinking and analysis
- Johns Hopkins John McGready:
Machine Learning
Specific Articles
- 2017-01 | Dermatologist-level classification of skin cancer with deep neural networks | Andre Esteva, Brett Kuprel, Roberto A. Novoa, Justin Ko, Susan M. Swetter, Helen M. Blau & Sebastian Thrun | Nature
Information
RNA-seq
- 2015-07 | How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets | Lucia Peixoto, Davide Risso, Shane G. Poplawski, Mathieu E. Wimmer, Terence P. Speed, Marcelo A. Wood, Ted Abel
R and Python
- Data Analysis in Python
- 2016 Dec Domino’s Chief Data Scientist, Eduardo Ariño de la Rubia
- Python
- Awesome Python
- Collecting Data:
- Feather Fast binary file format
- IBIS Unlock your data
- PARATEXT fast sane defaults
- BCOLZ When you have more data than RAM
- Visualization:
- Altair
- Bokeh interactive visualizations
- Geoplotlib geographical data
- Cleaning Data:
- Blaze numpy->ANY backend (DB, Cluster, etc...)
- xarray highly dimensional data (like Pandas)
- ** Dask** parallel computing
- Modeling:
- Keras high-level neural networks (skip tensorflow)
- PyMC3 Bayesian
- R Hadley Wickham,
- **Collecting Data:**A
- Feather
- Haven SAS, SPSS, or Stata data -> R tibbles
- readr (NO:read.csv) For floats/ints/NA
- JsonLight
- Visualization:
- ggplot2 ground-breaking updates
- htmlwidgets D3 brought to R via Javascript insert
- Leaflet
- tilegramR Scales to population
- Cleaning Data:
- dplyr
- broom (tidy|augment|glance)
- tidytext for nlp
- Modeling:
- MXNet
- TensorFlow Google's deep learning
- **Collecting Data:**A
- Python
Links
- How do project owners use pull requests on Github?
- NCBI
- GENCODE
- DrugBank
- UniProt
- OMIM Online Mendelian Inheritance in Man(R)
- UCSC
- Kegg
- HGNC HUGO Gene Nomenclature Committee
- HGDP population Allele Frequencies
- Matplotlib
GitHub
- Manage GitHub labels
- GitHub label colors
- Popular topics
- Explore
- Trending
- Most stars
- Max File Size:
- 100MB Max
- Use your bash history in Linux
Electrical Engineering
In a previous life...
- Dennis Feruson's answer for "How do capacitors go bad?
Misc.
- Amazon product search
- Learn to land an airplane if the pilot becomes incapacitated
- Memorize the 20 Amino Acids in 9 Minutes
- Anatomy & Physiology
- What do you call an acid with a bad attitude? A meano acid
- Did you hear that oxygen and potassium went on a date? I was OK.
Education is not the filling of a pail, but the lighting of a fire.
-William Butler Yeats
Copyright (C) 2015-present, DV Klopfenstein. All rights reserved.