The Marcotte Lab

protein_complex_maps

Kdrew's scripts for handling protein complex map data

MSblender

MSblender is a statistical tool for merging database search results from multiple database search engines for peptide identification based on a multivariate modeling approach.

SLICEM

appaloosa

Thin layer chromatography image analysis

plum

Generalizable phylogenetic latent variable models for ancestral network reconstruction

cfmsflow

diffrac

Scripts to analyze differential fractionation (DIF-FRAC) experiments

FluorosequencingImageAnalysis

Fluorosequencing Image Analysis code

pepliner

Pepliner: tools to visualize protein/peptide elutions

super.complex

Super.Complex is a supervised machine learning algorithm for community detection in networks. It learns information from known communities and uses this information to find new communities on the network.

MS_grouped_lookup

Scripts for looking up peptides with custom grouping for uniqueness

super.complex_website_humap

Interactive visualizations for protein complexes from hu.MAP 1.0 and hu.MAP 2.0 by Super.Complex and CORUM

whatprot

RL_complex_detection

Reinforcement learning community detection method using known communities

2D_projection_clustering

For 3D particle reconstruction, we cluster the particle's 2D projections in different orientations using pre-trained image embeddings and different clustering algorithms.

CoEVxIMP

scripts used in filtering evolutionary couplings to create IMP distance restraint

deBruijn_graphs

Scripts for the de Bruijn assembly of peptide kmers

FociFinder3D

hmm_proteome_annotation

iTF-seq

iTF-seq: Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches

leca-proteomics

Scripts & figures for the conserved eukaryotic interactome project

mycelium

Spring layout helper functions and demonstrations for iterative proximity ligation

pept-prot-infer

Tool for doing peptide and protein inference and quantitation on single molecule sequencing datasets, particularly on fluorosequencing data preprocessed by https://github.com/marcottelab/whatprot

peptide_elutions

Discovering proteolysis from peptide elutions

pivo

Proteomes Inferred Via Orthology

RL_humap_prediction

Interactive visualizations for protein complexes from hu.MAP 1.0 and hu.MAP 2.0 with RL

robust-fluorosequencing-plaster

Computational workflow described in robust-fluorosequencing publication

run_msblender

Wrapper for running MSBlender for an experiment with multiple mxZMLs

run_TPOT

simple wrapper for running TPOT

thesis_local_ml

David Yang's undergraduate thesis work