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@sheynkman-lab Lab for Proteoform Systems Biology

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    22 repositories

    • Mohi_MDS_LRP

      Public
      This repository is for LRP analysis for the Mohi Lab project focused on discovering proteoforms related to MDS.
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • chloe_project

      Public
      Python
      •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • zhang_mouse_aging

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • Alternative-Proteome-Detection-Project

      Public
      Python
      •0•1•0•0•Updated May 25, 2024May 25, 2024

    • biosurfer_analysis

      Public
      This repository reproduces the analysis for biosurfer tool
      Jupyter Notebook
      •0•1•0•0•Updated Mar 18, 2024Mar 18, 2024

    • biosurfer

      Public
      "Surf" the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.
      Python
      •
      MIT License
      •0•0•25•0•Updated Mar 15, 2024Mar 15, 2024

    • sheynkman-lab-docs

      Public
      0•0•0•0•Updated Aug 31, 2023Aug 31, 2023

    • pdb-isoform-analysis

      Public
      Comparison of all available PDB chains (human) to the alternative isoforms in GENCODE.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 12, 2023Jun 12, 2023

    • revio-mas-bulk-benchmark

      Public
      Python
      •0•0•0•0•Updated Jun 6, 2023Jun 6, 2023

    • sqtl_pipeline_v2

      Public
      Pipeline to map sQTLs to protein isoforms
      Python
      •2•0•0•0•Updated May 17, 2023May 17, 2023

    • Coon_isoform_analysis

      Public
      Looking at things related to data from https://www.nature.com/articles/s41587-023-01714-x#Sec24
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 4, 2023May 4, 2023

    • LIME

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Apr 16, 2023Apr 16, 2023

    • SMC_proteogenomics

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 7, 2023Apr 7, 2023

    • Biosurfer_BMD_analysis

      Public
      This code repository uses the Biosurfer tool (old version) to conduct NMD and protein truncation analysis for long-read bone proteogenomics project.
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 13, 2023Mar 13, 2023

    • Long-Read-Proteogenomics

      Public template
      A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
      nextflowproteomicsisoformslong-read-sequencingpipeline
      Python
      •
      MIT License
      •17•41•9•1•Updated Jan 18, 2023Jan 18, 2023

    • splice-event-to-isoform-pipeline

      Public
      Shay's splice event to isoform integration pipeline
      Python
      •
      MIT License
      •1•3•0•0•Updated Dec 2, 2022Dec 2, 2022

    • IsoSeq-Nextflow

      Public
      Nextflow implementation of IsoSeq3
      Python
      •
      MIT License
      •0•0•0•0•Updated May 20, 2022May 20, 2022

    • Huvec-Proteogenomic-Analysis

      Public
      HUVEC analysis analyzing proteogenomic data generated from long-read transcriptomic sequencing and bottom-up mass spec data
      Jupyter Notebook
      •0•0•0•0•Updated Apr 25, 2022Apr 25, 2022

    • Long-Read-Proteogenomics-Analysis

      Public
      Jupyter Notebook
      •1•5•1•0•Updated Jan 30, 2022Jan 30, 2022

    • tappAS

      Public
      This repository contains the source code for the tappAS application. See README for details.
      Java
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Nov 1, 2021Nov 1, 2021

    • sqanti3-docker

      Public
      A docker image to run SQANTI3
      Python
      •
      MIT License
      •5•0•0•0•Updated Aug 4, 2021Aug 4, 2021

    • SQANTI3_protein

      Public
      Repository of SQANTI3 tool for Quality Control of Long-Read Defined Transcriptomes
      Python
      •
      GNU General Public License v3.0
      •51•1•0•0•Updated Apr 16, 2021Apr 16, 2021