All

61 repositories

proximon-graph
Public
ProximonGraph constructs protein networks where nodes are homolog clusters and edges encode operonic adjacency, enabling detection of conserved gene neighborhoo…
Python
•
MIT License
•0•0•0•0•Updated Apr 28, 2026Apr 28, 2026
leca_notung_reconciliation
Public
Workflow for reconciling the presence of >10,000 orthogroups in the Last Eukaryotic Common Ancestor
Shell
•
Other
•0•0•0•0•Updated Apr 23, 2026Apr 23, 2026
protein_complex_maps
Public
Kdrew's scripts for handling protein complex map data
HTML
•
MIT License
•8•14•1•2•Updated Apr 23, 2026Apr 23, 2026
leca-proteomics
Public
Scripts & figures for the conserved eukaryotic interactome project
Jupyter Notebook
•0•0•0•0•Updated Apr 23, 2026Apr 23, 2026
MSblender
Public
MSblender is a statistical tool for merging database search results from multiple database search engines for peptide identification based on a multivariate mod…
Shell
•
MIT License
•6•8•1•0•Updated Apr 22, 2026Apr 22, 2026
whatprot
Public
C++
•
MIT License
•2•2•0•0•Updated Mar 26, 2025Mar 26, 2025
GuaPA
Public
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Dec 3, 2024Dec 3, 2024
peptide_elutions
Public
Discovering proteolysis from peptide elutions
R
•0•0•0•0•Updated Aug 16, 2024Aug 16, 2024
pept-prot-infer
Public
Tool for doing peptide and protein inference and quantitation on single molecule sequencing datasets, particularly on fluorosequencing data preprocessed by http…
Jupyter Notebook
•1•0•0•0•Updated Apr 22, 2024Apr 22, 2024
iTF-seq
Public
iTF-seq: Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches
Python
•0•0•0•0•Updated Feb 12, 2024Feb 12, 2024
cfmsflow
Public
Nextflow
•1•3•1•2•Updated Jul 6, 2023Jul 6, 2023
super.complex
Public
Super.Complex is a supervised machine learning algorithm for community detection in networks. It learns information from known communities and uses this informa…
distributed-computing community-detection community-detection-algorithm
distributed-computing community-detection community-detection-algorithm automl supervised-machine-learning supervised-clustering community-detection-evaluation community-detection-algorithms
Python
•
MIT License
•3•3•1•2•Updated Jul 6, 2023Jul 6, 2023
robust-fluorosequencing-plaster
Public
Computational workflow described in robust-fluorosequencing publication
Python
•
MIT License
•0•0•0•0•Updated May 30, 2023May 30, 2023
thesis_local_ml
Public
David Yang's undergraduate thesis work
0•0•0•0•Updated May 1, 2023May 1, 2023
RL_complex_detection
Public
Reinforcement learning community detection method using known communities
reinforcement-learning community-detection community-detection-algorithm
reinforcement-learning community-detection community-detection-algorithm protein-protein-interaction-network protein-complexes
Python
•
MIT License
•2•2•0•0•Updated Aug 3, 2022Aug 3, 2022
MS_grouped_lookup
Public
Scripts for looking up peptides with custom grouping for uniqueness
Python
•2•4•0•0•Updated Jul 27, 2022Jul 27, 2022
super.complex_website_humap
Public
Interactive visualizations for protein complexes from hu.MAP 1.0 and hu.MAP 2.0 by Super.Complex and CORUM
community-detection supervised-machine-learning protein-protein-interaction-network
community-detection supervised-machine-learning protein-protein-interaction-network protein-complexes protein-protein-interactions protein-complex-identification
HTML
•
MIT License
•1•2•0•0•Updated Jul 3, 2022Jul 3, 2022
2D_projection_clustering
Public
For 3D particle reconstruction, we cluster the particle's 2D projections in different orientations using pre-trained image embeddings and different clustering a…
Jupyter Notebook
•
MIT License
•1•0•0•0•Updated Jun 27, 2022Jun 27, 2022
RL_humap_prediction
Public
Interactive visualizations for protein complexes from hu.MAP 1.0 and hu.MAP 2.0 with RL
reinforcement-learning community-detection protein-protein-interaction-network
reinforcement-learning community-detection protein-protein-interaction-network protein-complexes protein-protein-interactions protein-complex-identification
HTML
•
MIT License
•2•0•0•0•Updated Jun 22, 2022Jun 22, 2022
diffrac
Public
Scripts to analyze differential fractionation (DIF-FRAC) experiments
Python
•
MIT License
•2•4•1•1•Updated Jun 9, 2022Jun 9, 2022
SLICEM
Public
Python
•
MIT License
•1•5•0•0•Updated Mar 15, 2021Mar 15, 2021
CoEVxIMP
Public
scripts used in filtering evolutionary couplings to create IMP distance restraint
Python
•3•0•0•0•Updated Jan 15, 2021Jan 15, 2021
pivo
Public
Proteomes Inferred Via Orthology
Python
•0•0•0•0•Updated Nov 20, 2020Nov 20, 2020
run_TPOT
Public
simple wrapper for running TPOT
Python
•1•0•0•0•Updated Sep 15, 2020Sep 15, 2020
deBruijn_graphs
Public
Scripts for the de Bruijn assembly of peptide kmers
HTML
•
MIT License
•0•0•0•0•Updated Jul 7, 2020Jul 7, 2020
run_msblender
Public
Wrapper for running MSBlender for an experiment with multiple mxZMLs
Shell
•0•0•0•0•Updated Dec 18, 2019Dec 18, 2019
FluorosequencingImageAnalysis
Public
Fluorosequencing Image Analysis code
Python
•
MIT License
•2•3•0•0•Updated Sep 9, 2019Sep 9, 2019
plum
Public
Generalizable phylogenetic latent variable models for ancestral network reconstruction
Python
•
MIT License
•0•4•0•0•Updated Aug 18, 2019Aug 18, 2019
appaloosa
Public
Thin layer chromatography image analysis
Python
•2•5•0•0•Updated May 30, 2019May 30, 2019
FociFinder3D
Public
Jupyter Notebook
•
MIT License
•2•0•0•0•Updated Dec 7, 2018Dec 7, 2018

ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

The Marcotte Lab

All

All

61 repositories

proximon-graph

leca_notung_reconciliation

protein_complex_maps

leca-proteomics

MSblender

whatprot

GuaPA

peptide_elutions

pept-prot-infer

iTF-seq

cfmsflow

super.complex

robust-fluorosequencing-plaster

thesis_local_ml

RL_complex_detection

MS_grouped_lookup

super.complex_website_humap

2D_projection_clustering

RL_humap_prediction

diffrac

SLICEM

CoEVxIMP

pivo

run_TPOT

deBruijn_graphs

run_msblender

FluorosequencingImageAnalysis

plum

appaloosa

FociFinder3D

All

All

Repositories list

61 repositories