Repositories list

• scUTRquant

  Public
  Bioinformatics pipeline for single-cell 3' UTR isoform quantification

  Python

  •

  GNU General Public License v3.0

  •44 forks•3232 stars•99 issues•00 pull requests•Updated Jan 29, 2026Jan 29, 2026

• mca-utrome

  Public
  3' UTR cleavage site identification from the Mouse Cell Atlas

  bioinformaticsscrna-seqalternative-polyadenylation+ 2

  bioinformaticsscrna-seqalternative-polyadenylationcleavage-sitessnakemake-pipeline

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 18, 2026Jan 18, 2026

• hcl-utrome

  Public
  generates human UTRome from Human Cell Landscape data

  R

  •00 forks•00 stars•11 issue•00 pull requests•Updated Jan 18, 2026Jan 18, 2026

• slam-k562-utrome

  Public
  Reprocesses SLAM-seq data from K562 using MWS UTRome

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 2, 2025Sep 2, 2025

• hcl-analysis

  Public
  Preprocesses Human Cell Landscape metadata and analyzes `hcl-utrome` final outputs

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 2, 2025Sep 2, 2025

• mca-analysis

  Public
  Preprocesses Mouse Cell Atlas metadata and analyzes `mca-utrome` final outputs

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 2, 2025Sep 2, 2025

• sommerkamp20

  Public
  Bioinformatics pipeline for 3'-seq data of Sommerkamp et al. 2020

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 2, 2025Sep 2, 2025

• tmuris-peaks

  Public
  Peak Width Analysis of the Tabula Muris Libraries

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 2, 2025Sep 2, 2025

• kallisto-overlap

  Public
  kallisto benchmarking of multi-UTR quantification for 3'-end tag-based RNA-seq

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 2, 2025Sep 2, 2025

• atlas-mm

  Public
  Merge and process multiple mouse 3' UTR datasets

  R

  •11 fork•00 stars•22 issues•00 pull requests•Updated Sep 2, 2025Sep 2, 2025

• atlas-hs

  Public
  Merge and process multiple human 3' UTR datasets

  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Sep 2, 2025Sep 2, 2025

• gwps-sq

  Public
  scUTRquant analysis of Genome-Wide Perturb-Seq dataset

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 2, 2025Sep 2, 2025

• scUTRquant-inputs

  Public
  Input definitions for the scUTRquant pipeline

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 2, 2025Sep 2, 2025

• txcutr-db

  Public
  Snakemake pipeline for generating truncated transcriptome annotations with txcutr

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 2, 2025Sep 2, 2025

• scUTRquant-figures

  Public
  Scripts used to generate figures for the scUTRquant manuscript

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 20, 2024Nov 20, 2024

• tiger-seq

  Public
  Computational analysis for Horste et al., Mol. Cell, 2023

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 2, 2024Jan 2, 2024

• cleavage-rate

  Public
  Pipeline to count reads in curated 3'-end mm10 peaks

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 16, 2021Jul 16, 2021

• utr-enhancers

  Public
  QAPA pipeline for enhancer-related RNA-seq datasets

  R

  •00 forks•11 star•22 issues•00 pull requests•Updated Jun 17, 2021Jun 17, 2021