Projects in Awesome Lists by fomightez

https://github.com/fomightez/sequencework

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

bioinformatics bioinformatics-analysis bioinformatics-scripts dna genomics list lists protein-sequences python rna

Last synced: 12 Apr 2025

https://github.com/fomightez/structurework

programs and scripts for molecular structure analysis

Last synced: 12 Apr 2025

https://github.com/fomightez/mini-pipelines

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

bash bioinformatics-pipeline pipelines pipelining python shell workflow-automation workflows

Last synced: 12 Apr 2025

https://github.com/fomightez/blast-binder

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

bioinformatics bioinformatics-analysis bioinformatics-scripts dna genomics pandas pandas-dataframe protein-sequences python rna

Last synced: 12 Apr 2025

https://github.com/fomightez/donut_plots_with_subgroups

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

Last synced: 12 Apr 2025

https://github.com/fomightez/pymol-binder

PyMOL able to be run via MyBinder.org

Last synced: 12 Apr 2025

https://github.com/fomightez/dataframe2img

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

Last synced: 12 Apr 2025

https://github.com/fomightez/animated_matplotlib_classic-binder

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

Last synced: 12 Apr 2025

https://github.com/fomightez/jupyter-rise_with-hide_code

Jupyter-rise working via MyBinder with hide_code enabled.

Last synced: 12 Apr 2025

https://github.com/fomightez/circos-binder

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

Last synced: 12 Apr 2025

https://github.com/fomightez/yeastmine

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

python

Last synced: 12 Apr 2025

https://github.com/fomightez/pdbepisa-binder

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

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts genomics nucleic-acids nucleic-sequence pandas pandas-dataframe protein-sequences protein-structure python snakemake

Last synced: 28 Dec 2024

https://github.com/fomightez/patmatch-binder

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

bioinformatics bioinformatics-analysis dna pandas protein-sequences rna

Last synced: 19 Feb 2025

https://github.com/fomightez/cyverse-talkpatmatchcircosvice

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

Last synced: 19 Feb 2025

https://github.com/fomightez/3dscatter_plot-binder

3D scatter plot examples via Binder

Last synced: 12 Apr 2025

https://github.com/fomightez/cairo-jupyter

Jupyter notebooks hosted via mybinder.org where cairo works

Last synced: 19 Feb 2025

https://github.com/fomightez/back_to_ipynb

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

Last synced: 28 Dec 2024

https://github.com/fomightez/methods_in_yeast_genetics

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

jupyter matplotlib python

Last synced: 19 Feb 2025

https://github.com/fomightez/b-roll-binder

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

Last synced: 19 Feb 2025

https://github.com/fomightez/cl_sq_demo-binder

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

Last synced: 19 Feb 2025

https://github.com/fomightez/mar2015feng_gr_m

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

Last synced: 19 Feb 2025

https://github.com/fomightez/pdbsum-binder

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

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts genomics pandas pandas-dataframes protein-sequences protein-structure python snakemake

Last synced: 12 Apr 2025

https://github.com/fomightez/rnartistcore-binder

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

Last synced: 19 Feb 2025

https://github.com/fomightez/dockerfiles

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

docker linux mac-osx

Last synced: 30 Mar 2025

https://github.com/fomightez/docker-mac-linuxchromium

Dockerfile for a container for Linux chromium with all dependencies that can be tunneled to Mac Desktop

bash docker dockerfile dockerfiles

Last synced: 19 Feb 2025

https://github.com/fomightez/pro-origami-binder

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

Last synced: 19 Feb 2025

https://github.com/fomightez/mcscan-binder

MCscan software available in a Jupyter environment running via the Binder service

Last synced: 19 Feb 2025

https://github.com/fomightez/synchro-binder

SynChro software available in a Jupyter environment running via the Binder service

Last synced: 19 Feb 2025

https://github.com/fomightez/salmondec2022

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

Last synced: 19 Feb 2025

https://github.com/fomightez/length_binder

Use Jupyter environment to look at protein length for various organisms. Active form served via Binder system.

Last synced: 19 Feb 2025

https://github.com/fomightez/pyscript_test

All the cool people are trying pyscript.

Last synced: 19 Feb 2025

https://github.com/fomightez/bernbiopython

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

Last synced: 19 Feb 2025

https://github.com/fomightez/ugene_help

helpful tips for working with Unipro's UGENE sequence analysis software

Last synced: 19 Feb 2025

https://github.com/fomightez/rayshader-binder

Binderized version of Tyler Morgan-Wall's Rayshader package https://www.rayshader.com/

Last synced: 19 Feb 2025

https://github.com/fomightez/3dsurface_plot-binder

3D surface plot examples via Binder

Last synced: 19 Feb 2025

https://github.com/fomightez/intermine-binder

Intermine Web Services available in a Jupyter environment running via the Binder service

Last synced: 19 Feb 2025

https://github.com/fomightez/cl_demo-binder

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

Last synced: 12 Apr 2025

https://github.com/fomightez/rnaseq_wang

Docker container for RNA-seq pipeline as described in Wang et al 2016 PMID:26483013

Last synced: 19 Feb 2025

https://github.com/fomightez/simple_appmode_binder

Last synced: 19 Feb 2025

https://github.com/fomightez/test_json_appmode

test json fixing appmode

Last synced: 19 Feb 2025

https://github.com/fomightez/proteomicswork

For utilities and code dealing with proteomics analysis

Last synced: 19 Feb 2025

https://github.com/fomightez/bendit-binder

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

Last synced: 19 Feb 2025

https://github.com/fomightez/plotdigitizer-binder

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

Last synced: 19 Feb 2025

https://github.com/fomightez/python_basics_4nanocourse

Python basics continued for Upstate Medical Spring 2020 nanocourse.

Last synced: 19 Feb 2025

https://github.com/fomightez/fomightez.github.io

Wayne's Portal for Bioinformatics Code Distribution via GitHub

Last synced: 19 Feb 2025

https://github.com/fomightez/usalign-binder

US-align running in MyBinder sessions

Last synced: 19 Feb 2025

https://github.com/fomightez/plotdigitizer-binderdesktop

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

Last synced: 19 Feb 2025

https://github.com/fomightez/pelican_configuration

configuration of pelican I have put together

Last synced: 19 Feb 2025

https://github.com/fomightez/3dscatter_plot_mod_playground-binder

Playground to test 3D scatter plot examples in modern JupyterLab and Jupyter Notebook via Binder

Last synced: 19 Feb 2025

https://github.com/fomightez/small_scale_ammonium_sulfate_precipitation_calculator

A tool facilitating designing a pilot experiment to screen for protein precipitation conditions.

Last synced: 19 Feb 2025

https://github.com/fomightez/tophat_and_bowtie

Tophat2 and Bowtie compatibility

bioinformatics bioinformatics-pipeline

Last synced: 19 Feb 2025

https://github.com/fomightez/photo2gps

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

Last synced: 19 Feb 2025

https://github.com/fomightez/mitcom-binder

Environment for working with MitCOM-related endeavors.

Last synced: 19 Feb 2025

https://github.com/fomightez/modal_labs_test

testing code at modal labs

Last synced: 19 Feb 2025

https://github.com/fomightez/webplotdigitizer-binder

see if the webplotdigitizer runs in a MyBinder session

Last synced: 19 Feb 2025

https://github.com/fomightez/guide_to_intermine-binder

Guide to getting started with using Intermine sites and Jupyter using MyBinder-served Jupyter notebooks.

Last synced: 19 Feb 2025

https://github.com/fomightez/python_basics_on_pdb_file

Python basics exploring a PDB file

Last synced: 19 Feb 2025

https://github.com/fomightez/simulated_data

A repository for code that generates various simulated data.

evolutionary expression gene phylogenetics phylogenomics python r rna-seq-analysis rna-seq-data simulated-data

Last synced: 19 Feb 2025

https://github.com/fomightez/bio3d-binder

launchable, working Jupyter-baseed environment with bio3d package for Biological Structure Analysis running in RStudio with some examples

Last synced: 19 Feb 2025

https://github.com/fomightez/appmode_plus

Last synced: 19 Feb 2025

https://github.com/fomightez/jan2015feng_gr_m

Feng lab meeting - Introduction to coding in Python workshop

python

Last synced: 19 Feb 2025