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Stars174
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Global Rank 136,846 (Top 5 %)
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Followers 148
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Following 177
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Registered over 11 years ago
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Most used languagesJupyter Notebook63.8 %Python24.1 %HTML3.4 %Shell3.4 %Dockerfile1.7 %CSS1.7 %Makefile 1.7 %
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Location 🇺🇸 United States
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Country Total Rank 31,435
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Country RankingJupyter Notebook1,902Dockerfile1,935Makefile 3,025
Top repositories
1
sequencework
programs and scripts, mainly python, for analyses related to nucleic or protein sequencesPython
22
2
blast-binder
Repo for running command line-based BLAST in Jupyter environment provided via Binder.Jupyter Notebook
7
3
pymol-binder
PyMOL able to be run via MyBinder.orgJupyter Notebook
6
4
animated_matplotlib_classic-binder
Notebook to demonstrate animated plots with Matplotlib in classic Jupyter notebook interface & NbClassic served via MyBinder system.Jupyter Notebook
6
5
donut_plots_with_subgroups
Several generalized scripts for making donut plots that include subgroups using dataframes and text tables as input.Jupyter Notebook
6
6
dataframe2img
Styled Pandas dataframe saved as an image that will be viewable when a Jupyter notebook is reloaded.Jupyter Notebook
6
7
3Dscatter_plot-binder
3D scatter plot examples via BinderJupyter Notebook
5
8
structurework
programs and scripts for molecular structure analysisPython
5
9
mini-pipelines
collection of scripts that chain together other scripts by preparing and processing/transforming data.Python
5
10
jupyter-rise_with-hide_code
Jupyter-rise working via MyBinder with hide_code enabled.Shell
5
11
yeastmine
using YeastMine (populated by SGD and powered by InterMine) to mine yeast Saccharomyces cerevisiae genetics dataPython
4
12
patmatch-binder
Repo for running command line-based PatMatch in Jupyter environment provided via Binder.Dockerfile
4
13
cyverse-talkPatMatchCircosVICE
Resource listing for accompanying Wayne's Cyverse talk on the PatMatch and Circos Binders and VICE apps.
4
14
circos-binder
Run Circos software in a Jupyter environment served by MyBinder.org.Jupyter Notebook
4
15
methods_in_yeast_genetics
a collection of Jupyter notebooks for doing calculations related to Methods in Yeast Genetics bookJupyter Notebook
3
16
text_mining
general text mining and text manipulation with Python scriptsPython
3
17
cairo-jupyter
Jupyter notebooks hosted via mybinder.org where cairo worksPython
3
18
back_to_ipynb
Conversion of the HTML representation of Jupyter notebook back to an `.ipynb` fileJupyter Notebook
3
19
pdbsum-binder
Demonstrating analysis of PDBsum-related data via active Jupyter sessions provided via MyBinder.orgJupyter Notebook
2
20
mar2015feng_gr_m
March 2015 Feng Lab group meeting - A Data Scientist's Toolbox for ChIP-Seq and BeyondPython
2
21
cl_sq_demo-binder
A collection of demonstrations of useful resources for command line / Jupyter session manipulation of sequence files.Jupyter Notebook
2
22
pdbepisa-binder
Using data from PDBePISA with the convenience of Python and Jupyter.Jupyter Notebook
2
23
RNArtistCore-binder
Launchable via MyBinder version of RNArtistCore, see https://github.com/fjossinet/RNArtistCoreJupyter Notebook
2
24
mcscan-binder
MCscan software available in a Jupyter environment running via the Binder serviceJupyter Notebook
2
25
Dockerfiles
organizational page for my various Dockerfiles I use on the desktop and on servers and on work stations
2
26
b-roll-binder
'for the future when the camera crew wants B-roll and asks you to sit at your desk "doing bioinformatics"'Shell
2
27
docker-mac-linuxchromium
Dockerfile for a container for Linux chromium with all dependencies that can be tunneled to Mac Desktop
2
28
UGENE_help
helpful tips for working with Unipro's UGENE sequence analysis softwarePython
1
29
jupyter_nb_basics
Very basic notebook to highlight some features of Jupyter Notebooks. Used on Retreat poster 2016.Jupyter Notebook
1
30
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
1
31
length_binder
Use Jupyter environment to look at protein length for various organisms. Active form served via Binder system.Jupyter Notebook
1
32
plotdigitizer-binder
Python-based PlotDigitizer working 'headless' in sessions served via MyBInder.orgJupyter Notebook
1
33
guide_to_intermine-binder
Guide to getting started with using Intermine sites and Jupyter using MyBinder-served Jupyter notebooks.
1
34
fomightez.github.io
Wayne's Portal for Bioinformatics Code Distribution via GitHubCSS
1
35
Python_basics_on_PDB_file
Python basics exploring a PDB fileJupyter Notebook
1
36
test_json_appmode
test json fixing appmodeJupyter Notebook
1
37
pelican_configuration
configuration of pelican I have put together
Makefile
1
38
de_jong-jupyter
getting Peter De Jong attractor plotting working in a Jupyter notebookJupyter Notebook
1
39
simple_appmode_binder
Jupyter Notebook
1
40
modal_labs_test
testing code at modal labsPython
1
41
plotdigitizer-binderDesktop
Python-based PlotDigitizer working alongside Qt on desktop in sessions served via MyBinder.orgPython
1
42
tophat_and_bowtie
Tophat2 and Bowtie compatibilityPython
1
43
rnaseq_wang
Docker container for RNA-seq pipeline as described in Wang et al 2016 PMID:26483013
1
44
proteomicswork
For utilities and code dealing with proteomics analysisPython
1
45
small_scale_ammonium_sulfate_precipitation_calculator
A tool facilitating designing a pilot experiment to screen for protein precipitation conditions.Jupyter Notebook
1
46
usalign-binder
US-align running in MyBinder sessionsJupyter Notebook
1
47
synchro-binder
SynChro software available in a Jupyter environment running via the Binder serviceJupyter Notebook
1
48
Python_basics_4nanocourse
Python basics continued for Upstate Medical Spring 2020 nanocourse.Jupyter Notebook
1
49
salmonDec2022
Trying Salmon Dec 2022, see https://www.biostars.org/p/98756/#9549038 and https://www.biostars.org/p/389360/
1
50
bendit-binder
Bend.it software to predict DNA curvature combined with Jupyter ecosystem served via MyBinder.orgJupyter Notebook
1
51
mitcom-binder
Environment for working with MitCOM-related endeavors.Jupyter Notebook
1
52
jan2015feng_gr_m
Feng lab meeting - Introduction to coding in Python workshopJupyter Notebook
1
53
appmode_plus
Jupyter Notebook
1
54
webplotdigitizer-binder
see if the webplotdigitizer runs in a MyBinder sessionJupyter Notebook
1
55
BernBiopython
Bernhard10's personal fork of biopython where he added parsing of missing residues from PDB headerPython
1
56
bio3d-binder
launchable, working Jupyter-baseed environment with bio3d package for Biological Structure Analysis running in RStudio with some examplesJupyter Notebook
1
57
cl_demo-binder
A collection of demonstrations of useful resources for command line / Jupyter session manipulation of structure files.Jupyter Notebook
1
58
borked_appmode_plus
Jupyter Notebook
1
59
pyscript_test
All the cool people are trying pyscript.HTML
1
60
photo2GPS
Launches an environment set up to make it easy to extract GPS coordinates from photo metadata.Jupyter Notebook
1
61
rayshader-binder
Binderized version of Tyler Morgan-Wall's Rayshader package https://www.rayshader.com/Jupyter Notebook
1
62
intermine-binder
Intermine Web Services available in a Jupyter environment running via the Binder serviceJupyter Notebook
1
63
simulated_data
A repository for code that generates various simulated data.Python
1
64
3Dsurface_plot-binder
3D surface plot examples via BinderHTML
1