Discover fomightez/UGENE_help Open Source project

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Created over 9 years ago
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helpful tips for working with Unipro's UGENE sequence analysis software

sequencework

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

Python

blast-binder

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

Jupyter Notebook

pymol-binder

PyMOL able to be run via MyBinder.org

Jupyter Notebook

animated_matplotlib_classic-binder

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

Jupyter Notebook

donut_plots_with_subgroups

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

Jupyter Notebook

dataframe2img

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

Jupyter Notebook

3Dscatter_plot-binder

3D scatter plot examples via Binder

Jupyter Notebook

structurework

programs and scripts for molecular structure analysis

Python

mini-pipelines

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

Python

jupyter-rise_with-hide_code

Jupyter-rise working via MyBinder with hide_code enabled.

Shell

yeastmine

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

Python

patmatch-binder

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

Dockerfile

cyverse-talkPatMatchCircosVICE

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

circos-binder

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

Jupyter Notebook

methods_in_yeast_genetics

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

Jupyter Notebook

text_mining

general text mining and text manipulation with Python scripts

Python

cairo-jupyter

Jupyter notebooks hosted via mybinder.org where cairo works

Python

back_to_ipynb

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

Jupyter Notebook

pdbsum-binder

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

Jupyter Notebook

mar2015feng_gr_m

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

Python

cl_sq_demo-binder

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

Jupyter Notebook

pdbepisa-binder

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

Jupyter Notebook

RNArtistCore-binder

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

Jupyter Notebook

mcscan-binder

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

Jupyter Notebook

Dockerfiles

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

b-roll-binder

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

Shell

docker-mac-linuxchromium

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

jupyter_nb_basics

Very basic notebook to highlight some features of Jupyter Notebooks. Used on Retreat poster 2016.

Jupyter Notebook

pro-origami-binder

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

Jupyter Notebook

length_binder

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

Jupyter Notebook

plotdigitizer-binder

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

Jupyter Notebook

guide_to_intermine-binder

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

fomightez.github.io

Wayne's Portal for Bioinformatics Code Distribution via GitHub

CSS

Python_basics_on_PDB_file

Python basics exploring a PDB file

Jupyter Notebook

test_json_appmode

test json fixing appmode

Jupyter Notebook

pelican_configuration

configuration of pelican I have put together

Makefile

de_jong-jupyter

getting Peter De Jong attractor plotting working in a Jupyter notebook

Jupyter Notebook

simple_appmode_binder

Jupyter Notebook

modal_labs_test

testing code at modal labs

Python

plotdigitizer-binderDesktop

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

Python

tophat_and_bowtie

Tophat2 and Bowtie compatibility

Python

rnaseq_wang

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

BernBiopython

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

Python

proteomicswork

For utilities and code dealing with proteomics analysis

Python

small_scale_ammonium_sulfate_precipitation_calculator

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

Jupyter Notebook

usalign-binder

US-align running in MyBinder sessions

Jupyter Notebook

synchro-binder

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

Jupyter Notebook

Python_basics_4nanocourse

Python basics continued for Upstate Medical Spring 2020 nanocourse.

Jupyter Notebook

salmonDec2022

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

bendit-binder

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

Jupyter Notebook

mitcom-binder

Environment for working with MitCOM-related endeavors.

Jupyter Notebook

jan2015feng_gr_m

Feng lab meeting - Introduction to coding in Python workshop

Jupyter Notebook

webplotdigitizer-binder

see if the webplotdigitizer runs in a MyBinder session

Jupyter Notebook

bio3d-binder

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

Jupyter Notebook

appmode_plus

Jupyter Notebook

cl_demo-binder

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

Jupyter Notebook

borked_appmode_plus

Jupyter Notebook

pyscript_test

All the cool people are trying pyscript.

HTML

photo2GPS

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

Jupyter Notebook

rayshader-binder

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

Jupyter Notebook

intermine-binder

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

Jupyter Notebook

simulated_data

A repository for code that generates various simulated data.

Python

3Dsurface_plot-binder

3D surface plot examples via Binder

HTML

fomightez/UGENE_help

fomightez

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