Repositories list

• 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 https://github.com/marcottelab/whatprot

  Jupyter Notebook

  •1•0•0•0•Updated Apr 22, 2024Apr 22, 2024

• leca-proteomics

  Public
  Scripts & figures for the conserved eukaryotic interactome project

  Jupyter Notebook

  •0•0•0•0•Updated Apr 8, 2024Apr 8, 2024

• whatprot

  Public
  C++

  •

  MIT License

  •2•2•0•0•Updated Feb 23, 2024Feb 23, 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

• protein_complex_maps

  Public
  Kdrew's scripts for handling protein complex map data

  HTML

  •

  MIT License

  •7•14•1•2•Updated Dec 13, 2023Dec 13, 2023

• MSblender

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

  Shell

  •

  MIT License

  •6•7•1•0•Updated Jul 31, 2023Jul 31, 2023

• cfmsflow

  Public
  Nextflow

  •1•3•0•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 information to find new communities on the network.

  distributed-computingcommunity-detectioncommunity-detection-algorithm+ 5automlsupervised-machine-learningsupervised-clusteringcommunity-detection-evaluationcommunity-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-learningcommunity-detectioncommunity-detection-algorithm+ 2protein-protein-interaction-networkprotein-complexes

  Python

  •

  MIT License

  •2•1•0•0•Updated Aug 3, 2022Aug 3, 2022

• MS_grouped_lookup

  Public
  Scripts for looking up peptides with custom grouping for uniqueness

  Python

  •2•3•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-detectionsupervised-machine-learningprotein-protein-interaction-network+ 3protein-complexesprotein-protein-interactionsprotein-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 algorithms.

  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-learningcommunity-detectionprotein-protein-interaction-network+ 3protein-complexesprotein-protein-interactionsprotein-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

  •1•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•4•0•0•Updated May 30, 2019May 30, 2019

• FociFinder3D

  Public
  Jupyter Notebook

  •

  MIT License

  •2•0•0•0•Updated Dec 7, 2018Dec 7, 2018

• mycelium

  Public
  Spring layout helper functions and demonstrations for iterative proximity ligation

  Jupyter Notebook

  •0•0•0•0•Updated Nov 14, 2018Nov 14, 2018

• hmm_proteome_annotation

  Public
  Shell

  •0•0•0•0•Updated Aug 26, 2018Aug 26, 2018

• pepliner

  Public
  Pepliner: tools to visualize protein/peptide elutions

  HTML

  •

  Other

  •0•3•0•0•Updated Jul 27, 2018Jul 27, 2018