Wayne's Bioinformatics Code Portal

sequencework. programs and scripts, mainly python, for analyses related to nucleic or protein sequences

structurework. programs and scripts for molecular structure analysis

mini-pipelines. collection of scripts that chain together other scripts by preparing and processing/transforming data.

pdbepisa-binder. Using data from PDBePISA with the convenience of Python and Jupyter.

pymol-binder. PyMOL able to be run via MyBinder.org

donut_plots_with_subgroups. Several generalized scripts for making donut plots that include subgroups using dataframes and text tables as input.

dataframe2img. Styled Pandas dataframe saved as an image that will be viewable when a Jupyter notebook is reloaded.

blast-binder. Repo for running command line-based BLAST in Jupyter environment provided via Binder.

pro-origami-binder. Alex Stivala & colleagues' Pro-origami software for making protein structure wiring diagrams bundled up for use via MyBinder-served Jupyter sessions.

animated_matplotlib_classic-binder. Notebook to demonstrate animated plots with Matplotlib in classic Jupyter notebook interface & NbClassic served via MyBinder system.

jupyter-rise_with-hide_code. Jupyter-rise working via MyBinder with hide_code enabled.

yeastmine. using YeastMine (populated by SGD and powered by InterMine) to mine yeast Saccharomyces cerevisiae genetics data

circos-binder. Run Circos software in a Jupyter environment served by MyBinder.org.

text_mining. general text mining and text manipulation with Python scripts

communication_voila. a number of demonstrations of plots and ipywidgets widgets in notebooks and Voila

patmatch-binder. Repo for running command line-based PatMatch in Jupyter environment provided via Binder.

cyverse-talkPatMatchCircosVICE. Resource listing for accompanying Wayne's Cyverse talk on the PatMatch and Circos Binders and VICE apps.

3Dscatter_plot-binder. 3D scatter plot examples via Binder

back_to_ipynb. Conversion of the HTML representation of Jupyter notebook back to an `.ipynb` file

methods_in_yeast_genetics. a collection of Jupyter notebooks for doing calculations related to Methods in Yeast Genetics book

cairo-jupyter. Jupyter notebooks hosted via mybinder.org where cairo works

mcscan-binder. MCscan software available in a Jupyter environment running via the Binder service

pdbsum-binder. Demonstrating analysis of PDBsum-related data via active Jupyter sessions provided via MyBinder.org

docker-mac-linuxchromium. Dockerfile for a container for Linux chromium with all dependencies that can be tunneled to Mac Desktop

RNArtistCore-binder. Launchable via MyBinder version of RNArtistCore, see https://github.com/fjossinet/RNArtistCore

mar2015feng_gr_m. March 2015 Feng Lab group meeting - A Data Scientist's Toolbox for ChIP-Seq and Beyond

b-roll-binder. 'for the future when the camera crew wants B-roll and asks you to sit at your desk "doing bioinformatics"'

cl_sq_demo-binder. A collection of demonstrations of useful resources for command line / Jupyter session manipulation of sequence files.

Dockerfiles. organizational page for my various Dockerfiles I use on the desktop and on servers and on work stations

tophat_and_bowtie. Tophat2 and Bowtie compatibility

bear-classifier. Jupyter Notebook

plotdigitizer-binder. Python-based PlotDigitizer working 'headless' in sessions served via MyBInder.org

voila-gallery.github.io. Public facing deployment for voila-gallery.org

pyscript_test. All the cool people are trying pyscript.

3Dsurface_plot-binder. 3D surface plot examples via Binder

test_json_appmode. test json fixing appmode

appmode_plus. Jupyter Notebook

salmonDec2022. Trying Salmon Dec 2022, see https://www.biostars.org/p/98756/#9549038 and https://www.biostars.org/p/389360/

borked_appmode_plus. Jupyter Notebook

proteomicswork. For utilities and code dealing with proteomics analysis

rich-dataframe. Create pretty Pandas Dataframe (I didn't care about the animated aspect so it has been removed so works in Jupyter better.)

pyMSAviz. MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

usalign-binder. US-align running in MyBinder sessions

modal_labs_test. testing code at modal labs

mitcom-binder. Environment for working with MitCOM-related endeavors.

webplotdigitizer-binder. see if the webplotdigitizer runs in a MyBinder session

binder_trial. Jupyter Notebook

plotdigitizer-binderDesktop. Python-based PlotDigitizer working alongside Qt on desktop in sessions served via MyBinder.org

ghana. Leveraging the healthwork force to increase Covid vaccine uptake in Ghana

appmode. Creating web applications with Jupyter and Binder

cl_demo-binder. A collection of demonstrations of useful resources for command line / Jupyter session manipulation of structure files.

r_phylogenetics_worshop. Using ggtree to build phylogenetic trees

jupyter-desktop-server. Run a Linux Desktop on a JupyterHub

Python_basics_on_PDB_file. Python basics exploring a PDB file

BernBiopython. Bernhard10's personal fork of biopython where he added parsing of missing residues from PDB header

Python_basics_4nanocourse. Python basics continued for Upstate Medical Spring 2020 nanocourse.

gel_image_annotation. Simple script for automatically annotating SDS-PAGE gel images

photo2GPS. Launches an environment set up to make it easy to extract GPS coordinates from photo metadata.

bendit-binder. Bend.it software to predict DNA curvature combined with Jupyter ecosystem served via MyBinder.org