Owner

Benjamin-Lee

5 indexed repositories · View on GitHub

deep-rules
Ten Quick Tips for Deep Learning in Biology

HTML · 226 stars
CodonAdaptationIndex
Python Implementation of Codon Adaption Index

Jupyter Notebook · 38 stars
vdsearch
Viroid-like circRNA discovery and analysis suite

Python · 20 stars
DNAvisualization.org
🧬📈 Turn DNA sequences into interactive visualizations

Vue · 13 stars
viroiddb
A curated database of all available viroid-like RNA sequences

Vue · 5 stars

Beginner friendly Everything

Open All

absent amino acids Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Benjamin-Lee/CodonAdaptationIndex#18 · 1 comment · Opened Dec 4, 2025
Running error, can you help to see it Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

Benjamin-Lee/vdsearch#16 · 2 comments · Opened Aug 8, 2025
Any advice on how to install vdsearch on Google Colab Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Benjamin-Lee/vdsearch#15 · 1 comment · Opened May 6, 2024
Is rnamotif mandatory? how do i complement it to the software? Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

Benjamin-Lee/vdsearch#13 · 1 comment · Opened Nov 9, 2023
Installation error: nimporter.NimCompileException: cannot open file: cello Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Benjamin-Lee/vdsearch#12 · 1 comment · 1 reaction · Opened Apr 4, 2023
[Request] Conda installable Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Benjamin-Lee/vdsearch#8 · 2 comments · Opened Feb 2, 2023
Download CMs when Infernal command needs them and they're not provided or cached Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

Benjamin-Lee/vdsearch#6 · Opened Feb 26, 2022
Automatically purge the cache on a version update Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

Benjamin-Lee/vdsearch#5 · Opened Feb 26, 2022
Parallelize find_circs Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/vdsearch#4 · Opened Feb 26, 2022
Add a command to predict structures of sequences Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/vdsearch#3 · Opened Feb 26, 2022
Enable support for configurable minimum identity and seed length in find_circs Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

Benjamin-Lee/vdsearch#2 · Opened Feb 26, 2022
Kill the easy-search pipeline if the number of circRNAs is zero Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Benjamin-Lee/vdsearch#1 · Opened Feb 26, 2022
pip install not working Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

Benjamin-Lee/CodonAdaptationIndex#14 · 17 comments · Opened Sep 16, 2021
Link out to NCBI GenBank page for each rotationally identical sequence Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

Benjamin-Lee/viroiddb#55 · Opened Jul 1, 2021
sequence list page - color coding types and more Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Benjamin-Lee/viroiddb#49 · 1 comment · Opened Jun 30, 2021
Add copy/download buttons to Infernal output Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

Benjamin-Lee/viroiddb#48 · Opened Jun 30, 2021
Unify + and - SS view Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

Benjamin-Lee/viroiddb#42 · Opened Jun 29, 2021
Add clear results button to search Open

Benjamin-Lee/viroiddb#39 · 1 comment · 1 assignee · Opened Jun 28, 2021
Sequence viewer flukes Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/viroiddb#21 · 1 comment · Opened Jun 17, 2021
Sequence hub flukes Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Benjamin-Lee/viroiddb#15 · Opened Jun 14, 2021
Add page with direct data download links Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

Benjamin-Lee/viroiddb#2 · Opened Jun 4, 2021
Add page listing versions and changes Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Benjamin-Lee/viroiddb#1 · Opened Jun 4, 2021
mlf-core: a framework for deterministic machine learning Open

paper

Difficulty 1/5 1-3 hours Newbie friendliness 35/100

Benjamin-Lee/deep-rules#361 · 1 comment · Opened May 14, 2021
Conda package Open

enhancement

Difficulty 1/5 Under an hour Newbie friendliness 25/100

Benjamin-Lee/CodonAdaptationIndex#13 · 2 reactions · Opened May 5, 2021
Method doesn't default to yau Open

low priority

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Benjamin-Lee/DNAvisualization.org#198 · Opened Jan 25, 2021
Add a jupyter notebook to docs or tests Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

Benjamin-Lee/CodonAdaptationIndex#11 · 3 comments · Opened Jan 1, 2021
If sequence names are too long, don't show them in the title but do show the legend Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Benjamin-Lee/DNAvisualization.org#186 · Opened Dec 24, 2020
Zooming in on a region when there's no sequence there still produces points Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Benjamin-Lee/DNAvisualization.org#185 · Opened Dec 24, 2020
Normalize citation formats Open

low priority

Benjamin-Lee/DNAvisualization.org#184 · 1 assignee · Opened Dec 23, 2020
Zoom on Gates fails Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 20/100

Benjamin-Lee/DNAvisualization.org#176 · Opened Dec 19, 2020
Showing a spinner breaks updating when zooming in after changing Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

Benjamin-Lee/DNAvisualization.org#175 · Opened Dec 19, 2020
Only show spinner when there's no precomputed 10k visualization Open

low priority

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

Benjamin-Lee/DNAvisualization.org#173 · Opened Dec 18, 2020
Close modal appears twice Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 20/100

Benjamin-Lee/DNAvisualization.org#170 · 1 comment · Opened Dec 18, 2020
Move visualization to a new route Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 25/100

Benjamin-Lee/DNAvisualization.org#169 · 1 comment · Opened Dec 18, 2020
Delete axios Open

low priority

Benjamin-Lee/DNAvisualization.org#161 · 1 assignee · Opened Dec 18, 2020
Move WASM to a WebWorker Open

enhancement requirement

Difficulty 4/5 3-5 days Newbie friendliness 20/100

Benjamin-Lee/DNAvisualization.org#149 · Opened Dec 16, 2020
Zooming in ignores disabled legend items Open

low priority

Difficulty 3/5 1-2 days Newbie friendliness 25/100

Benjamin-Lee/DNAvisualization.org#146 · Opened Dec 16, 2020
Show sequence names on hover in file mode Open

low priority

Difficulty 3/5 1-2 days Newbie friendliness 20/100

Benjamin-Lee/DNAvisualization.org#145 · Opened Dec 16, 2020
Show error when file is too large Open

low priority

Benjamin-Lee/DNAvisualization.org#144 · 1 assignee · Opened Dec 16, 2020
Change the method picker from a b-button-group to a b-radio Open

low priority

Difficulty 2/5 1-3 hours Newbie friendliness 25/100

Benjamin-Lee/DNAvisualization.org#143 · Opened Dec 15, 2020
Add GC content visualization Open

enhancement low priority

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/DNAvisualization.org#142 · 4 comments · Opened Dec 15, 2020
Add support for changing file uploaded file names Open

low priority

Difficulty 4/5 3-5 days Newbie friendliness 20/100

Benjamin-Lee/DNAvisualization.org#138 · Opened Dec 15, 2020
Automatically decide whether to use sequence mode or file mode Open

low priority

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/DNAvisualization.org#136 · Opened Dec 15, 2020
Fix leaking WASM memory Open

low priority

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Benjamin-Lee/DNAvisualization.org#124 · Opened Dec 13, 2020
Add list of citations Open

enhancement

Benjamin-Lee/DNAvisualization.org#123 · 1 comment · 1 assignee · Opened Dec 13, 2020
Convert Gates, Randic, and Qi to i32 Open

low priority

Difficulty 3/5 1-2 days Newbie friendliness 25/100

Benjamin-Lee/DNAvisualization.org#122 · 1 comment · Opened Dec 13, 2020
Fix WASM switch cases to support lowercase Open

low priority

Difficulty 2/5 1-3 hours Newbie friendliness 30/100

Benjamin-Lee/DNAvisualization.org#117 · 1 comment · Opened Dec 12, 2020
Make y zooming work Open

low priority

Difficulty 4/5 3-5 days Newbie friendliness 15/100

Benjamin-Lee/DNAvisualization.org#103 · Opened Dec 10, 2020
Give specific example of relevant metrics for overfitting Open

Difficulty 2/5 1-3 hours Newbie friendliness 25/100

Benjamin-Lee/deep-rules#267 · Opened Oct 13, 2020
Outstanding issues not specific to any tips Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/deep-rules#252 · 10 comments · Opened Oct 7, 2020

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