Owner

LewisLabUCSD

9 indexed repositories · View on GitHub

Ligand-Receptor-Pairs
Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.

155 stars
MammalianSecretoryRecon
Secretory Pathway Reconstruction for Human, CHO, and Mouse

Jupyter Notebook · 12 stars
PinAPL-Py
A no hassle tool for analyzing your favorite CRISPR screen dataset!

Python · 11 stars
GlyCompare
Comparing glycoprofiles, leveraging motif substructure arithmetic

Jupyter Notebook · 10 stars
StanDep
Code for StanDep Paper

MATLAB · 5 stars
RegressionModelPipeline
Pipeline for feature selection, interaction assessment, regression modeling and prediction assessment for 1-1000s of features

R · 4 stars
GlyCompareCT
glyCompare command line tool

Python · 3 stars
iGSEA
Wrap code for runing GSEA analysis

R · 2 stars
Mito_Trace
Tracking cell-lineage using mutations in the mitochondrion genome.

Jupyter Notebook · 0 stars

Beginner friendly Everything

Open All

Issues with running example data sets Open

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

LewisLabUCSD/GlyCompareCT#3 · 1 comment · Opened May 3, 2024
Problem with opening a file Open

Difficulty 1/5 Under an hour Newbie friendliness 20/100

LewisLabUCSD/Ligand-Receptor-Pairs#2 · 4 comments · Opened Feb 19, 2024
Mistake of the files Open

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

LewisLabUCSD/Ligand-Receptor-Pairs#1 · 1 comment · Opened Jul 10, 2023
How to install ”iGSEA“ in Rstudio? Open

Difficulty 1/5 Under an hour Newbie friendliness 30/100

LewisLabUCSD/iGSEA#2 · Opened Oct 16, 2022
How do I run these scripts on Linux? The Web-application is not working. Open

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

LewisLabUCSD/PinAPL-Py#2 · 2 comments · Opened Mar 29, 2022
Missing file for the Quick Example run Open

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

LewisLabUCSD/GlyCompare#16 · 1 comment · Opened Jan 3, 2022
growth of poisson refactor Open

todo

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

LewisLabUCSD/Mito_Trace#49 · Opened May 25, 2021
Add the MT clone map so it can contain multiple mutants in lineages Open

todo

Difficulty 5/5 Over a week Newbie friendliness 25/100

LewisLabUCSD/Mito_Trace#48 · Opened May 25, 2021
Add the MT clone map so it can contain multiple mutants in lineages Open

todo

Difficulty 5/5 Over a week Newbie friendliness 25/100

LewisLabUCSD/Mito_Trace#46 · Opened May 25, 2021
account for mt_pos being a list not an int Open

todo

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

LewisLabUCSD/Mito_Trace#45 · Opened May 25, 2021
This should be in mro/common for general use Open

todo

Difficulty 4/5 3-5 days Newbie friendliness 35/100

LewisLabUCSD/Mito_Trace#44 · Opened May 25, 2021
account for mt_pos being a list not an int Open

todo

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

LewisLabUCSD/Mito_Trace#37 · Opened Dec 10, 2020
This should be in mro/common for general use Open

todo

Difficulty 4/5 3-5 days Newbie friendliness 35/100

LewisLabUCSD/Mito_Trace#36 · Opened Dec 10, 2020
This should be in mro/common for general use Open

todo

Difficulty 4/5 3-5 days Newbie friendliness 32/100

LewisLabUCSD/Mito_Trace#35 · Opened Dec 10, 2020
Refactor metrics part of the simulation class to a separate class Open

enhancement

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

LewisLabUCSD/Mito_Trace#32 · Opened Oct 28, 2020
Implement Cassiopeida Open

good first issue

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

LewisLabUCSD/Mito_Trace#31 · Opened Oct 28, 2020
Implement mgatk Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

LewisLabUCSD/Mito_Trace#30 · Opened Oct 28, 2020
growth of poisson refactor Open

todo

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

LewisLabUCSD/Mito_Trace#28 · Opened Oct 27, 2020
account for mt_pos being a list not an int Open

todo

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

LewisLabUCSD/Mito_Trace#25 · Opened Oct 27, 2020
Running simulation overflows RAM Open

enhancement

LewisLabUCSD/Mito_Trace#23 · 1 assignee · Opened Oct 27, 2020
Simulation with new MT mutants Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

LewisLabUCSD/Mito_Trace#22 · Opened Oct 27, 2020
Writeup for Simulation Open

documentation

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

LewisLabUCSD/Mito_Trace#21 · Opened Oct 27, 2020
Kmeans Clustering simulation results Open

todo

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

LewisLabUCSD/Mito_Trace#20 · 1 comment · Opened Oct 27, 2020
Simulation Run Open

Epic

Difficulty 5/5 Over a week Newbie friendliness 25/100

LewisLabUCSD/Mito_Trace#19 · Opened Oct 27, 2020
account for mt_pos being a list not an int Open

todo

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

LewisLabUCSD/Mito_Trace#15 · Opened Oct 26, 2020
Add the MT clone map that can contain multiple mutants in lineages Open

todo

Difficulty 5/5 Over a week Newbie friendliness 25/100

LewisLabUCSD/Mito_Trace#6 · Opened Oct 21, 2020
Fuc(1) is not in Fuc(2) Open

LewisLabUCSD/GlyCompare#13 · 1 assignee · Opened Sep 3, 2020
File experimental_constraints.mat missing Open

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

LewisLabUCSD/MammalianSecretoryRecon#1 · Opened Jun 12, 2020
From bam to UMIs and cell filter Open

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

LewisLabUCSD/Mito_Trace#1 · 1 comment · Opened Feb 4, 2020
What's the difference between a root and a core? If they are the same, then couldn't it be better if core was changed to root? Open

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

LewisLabUCSD/GlyCompare#8 · 2 comments · Opened Aug 19, 2019
```complex``` and ```simple``` are the same variable, unify nomenclature Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

LewisLabUCSD/GlyCompare#7 · Opened Jul 9, 2019
Plotting functionality Open

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

LewisLabUCSD/StanDep#11 · Opened May 1, 2019
TODO: add context variables Open

LewisLabUCSD/RegressionModelPipeline#3 · 1 assignee · Opened Oct 24, 2016
TODO: generalize stepwise_multivariate_model_selection Open

LewisLabUCSD/RegressionModelPipeline#2 · 1 assignee · Opened Oct 24, 2016
TODO: impliment many_to_few Open

LewisLabUCSD/RegressionModelPipeline#1 · 1 assignee · Opened Oct 24, 2016

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