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    33 repositories

    • snakemake_references

      Public
      Python
      •0•1•0•0•Updated Mar 2, 2026Mar 2, 2026

    • tcga-skcm-r2-gtex-analysis

      Public
      R
      •0•0•0•0•Updated Feb 6, 2026Feb 6, 2026

    • stellarscope

      Public
      Single-cell Transposable Element Locus Level Analysis of scRNA Sequencing
      Jupyter Notebook
      •
      MIT License
      •5•21•20•0•Updated Oct 28, 2025Oct 28, 2025

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.9k•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • awesome-transposable-elements

      Public
      A curated list of software packages, databases, and resources for transposable element (TE) research in genomics
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Sep 11, 2025Sep 11, 2025

    • HERV_GCB_Bulk

      Public
      Analysis of bulk RNA-Seq data from the Germinal Center.
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 21, 2025Apr 21, 2025

    • follicular_lymphoma_TE_atlas

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 21, 2025Apr 21, 2025

    • burkitt_lymphoma_TE_atlas

      Public
      TE quantification (Telescope) pipeline for Burkitt Lymphoma bulk RNA-seq samples
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 21, 2025Apr 21, 2025

    • DLBCL_HERV_atlas_GDC

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 21, 2025Apr 21, 2025

    • HOPE_informatics_core

      Public
      MIT License
      •0•0•0•0•Updated Nov 20, 2024Nov 20, 2024

    • HERV_scGTEX

      Public
      Quantify HERVs in single nucleus RNA-seq GTEx datasets using single-cell Telescope (scTelescope)
      Python
      •
      MIT License
      •0•0•2•0•Updated Dec 27, 2023Dec 27, 2023

    • HERV_scGCB

      Public
      Single cell data from Germinal Center B cell paper
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 11, 2023Dec 11, 2023

    • TCGA_SKCM_mets

      Public
      The Repository to download, STAR_align, TELESCOPE and Process DE for Mets vs. Non-mets TCGA CM Bulk-RNAseq
      Jupyter Notebook
      •0•0•0•0•Updated Oct 24, 2023Oct 24, 2023

    • TelescopeTools

      Public
      What the Package Does (One Line, Title Case)
      R
      •
      Other
      •0•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • Mets_CM_bulk

      Public
      Bulk RNA seq analysis for responders v non-responders
      Python
      •0•0•0•0•Updated Aug 15, 2023Aug 15, 2023

    • teabiscuit

      Public
      Transposable Element Analysis in BraIn, Single Cell, and Ubiquitous Tissues
      Creative Commons Attribution 4.0 International
      •1•0•0•0•Updated May 24, 2023May 24, 2023

    • nixonlab.github.io

      Public
      HTML
      •0•0•0•0•Updated May 12, 2023May 12, 2023

    • StellarscopeTools

      Public
      Other
      •0•0•0•0•Updated May 12, 2023May 12, 2023

    • bioinformatics_tips

      Public
      General bioinformatics tips
      Creative Commons Zero v1.0 Universal
      •0•2•0•0•Updated Mar 29, 2023Mar 29, 2023

    • HERV_um_mets

      Public
      HERV analysis in UM metastasis
      Python
      •0•0•0•0•Updated Mar 27, 2023Mar 27, 2023

    • te_riboseq_atlas

      Public
      A transposable element atlas of ribo-seq data from multiple tissue types. (Project ID: PRJNA756018)
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 15, 2023Feb 15, 2023

    • snakemake_rule_library

      Public
      A place to share generic "best practices" rules for the lab
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 27, 2023Jan 27, 2023

    • dopkins_jan2022

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 24, 2022Dec 24, 2022

    • scopetools

      Public
      Utility functions for working with Telescope and Stellarscope data
      R
      •
      Other
      •0•1•2•0•Updated Sep 28, 2022Sep 28, 2022

    • stellarscope_bug_reproduce

      Public
      Shell
      •0•0•0•0•Updated Aug 15, 2022Aug 15, 2022

    • stellarscope_simulation

      Public
      Simulations for testing Stellarscope
      MIT License
      •0•0•0•0•Updated Jul 1, 2022Jul 1, 2022

    • snakemake-wrappers

      Public
      This is the development home of the Snakemake wrapper repository, see
      Python
      •212•0•0•0•Updated Nov 11, 2021Nov 11, 2021

    • scTelescope

      Public
      Quantify HERVs in single-cell sequencing data
      Python
      •
      MIT License
      •0•1•1•0•Updated Sep 30, 2021Sep 30, 2021

    • documenting-scTELESCOPE

      Public
      A place to keep articles, datasets, and notes related to the development of scTELESCOPE
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 28, 2021Sep 28, 2021

    • NCICCR

      Public
      data from national cancer institute for cancer research
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 28, 2021Sep 28, 2021
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