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    18 repositories

    • scUTRquant-figures

      Public
      Scripts used to generate figures for the scUTRquant manuscript
      HTML
      •0•0•0•0•Updated Nov 20, 2024Nov 20, 2024

    • scUTRquant

      Public
      Bioinformatics pipeline for single-cell 3' UTR isoform quantification
      Python
      •
      GNU General Public License v3.0
      •4•16•13•0•Updated Nov 20, 2024Nov 20, 2024

    • txcutr-db

      Public
      Snakemake pipeline for generating truncated transcriptome annotations with txcutr
      Python
      •0•0•0•0•Updated Aug 1, 2024Aug 1, 2024

    • scUTRquant-inputs

      Public
      Input definitions for the scUTRquant pipeline
      Python
      •0•0•0•0•Updated Mar 31, 2024Mar 31, 2024

    • gwps-sq

      Public
      scUTRquant analysis of Genome-Wide Perturb-Seq dataset
      HTML
      •0•0•0•0•Updated Mar 29, 2024Mar 29, 2024

    • atlas-hs

      Public
      Merge and process multiple human 3' UTR datasets
      R
      •1•0•0•0•Updated Mar 29, 2024Mar 29, 2024

    • atlas-mm

      Public
      Merge and process multiple mouse 3' UTR datasets
      R
      •1•0•2•0•Updated Mar 29, 2024Mar 29, 2024

    • kallisto-overlap

      Public
      kallisto benchmarking of multi-UTR quantification for 3'-end tag-based RNA-seq
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 29, 2024Mar 29, 2024

    • tmuris-peaks

      Public
      Peak Width Analysis of the Tabula Muris Libraries
      Jupyter Notebook
      •0•0•0•0•Updated Mar 29, 2024Mar 29, 2024

    • sommerkamp20

      Public
      Bioinformatics pipeline for 3'-seq data of Sommerkamp et al. 2020
      HTML
      •0•0•0•0•Updated Mar 28, 2024Mar 28, 2024

    • mca-analysis

      Public
      Preprocesses Mouse Cell Atlas metadata and analyzes `mca-utrome` final outputs
      HTML
      •0•0•0•0•Updated Mar 28, 2024Mar 28, 2024

    • hcl-analysis

      Public
      Preprocesses Human Cell Landscape metadata and analyzes `hcl-utrome` final outputs
      HTML
      •0•0•0•0•Updated Mar 28, 2024Mar 28, 2024

    • hcl-utrome

      Public
      generates human UTRome from Human Cell Landscape data
      R
      •0•0•0•0•Updated Mar 27, 2024Mar 27, 2024

    • slam-k562-utrome

      Public
      Reprocesses SLAM-seq data from K562 using MWS UTRome
      HTML
      •0•0•0•0•Updated Mar 27, 2024Mar 27, 2024

    • tiger-seq

      Public
      Computational analysis for Horste et al., Mol. Cell, 2023
      HTML
      •0•0•0•0•Updated Jan 2, 2024Jan 2, 2024

    • mca-utrome

      Public
      3' UTR cleavage site identification from the Mouse Cell Atlas
      bioinformaticsscrna-seqalternative-polyadenylationcleavage-sitessnakemake-pipeline
      R
      •0•0•0•0•Updated Jul 5, 2023Jul 5, 2023

    • cleavage-rate

      Public
      Pipeline to count reads in curated 3'-end mm10 peaks
      Python
      •0•0•0•0•Updated Jul 16, 2021Jul 16, 2021

    • utr-enhancers

      Public
      QAPA pipeline for enhancer-related RNA-seq datasets
      R
      •0•1•2•0•Updated Jun 17, 2021Jun 17, 2021