Repositories list

• aa-tRNA-seq-pipeline

  Public
  Snakemake pipeline to process nanopore aa-tRNA-seq data

  rna-seqsnakemakenanopore-sequencing

  Python

  •

  MIT License

  •2•3•8•3•Updated Jan 22, 2026Jan 22, 2026

• 2a-peptide-search

  Public
  HMM models of the 2A peptide and DB search results

  Python

  •0•0•2•1•Updated Jan 18, 2026Jan 18, 2026

• ucsc_snapshots

  Public
  Robotically fetch images for specified regions from the UCSC Genome Browser

  Python

  •0•5•0•0•Updated Jan 18, 2026Jan 18, 2026

• aform-rs

  Public
  TUI for Stockholm MSA viz/edit

  rna-structuremsastockholm+ 1tui-rs

  Rust

  •0•0•2•0•Updated Jan 17, 2026Jan 17, 2026

• valr

  Public
  Genome Interval Arithmetic in R

  genomeinterval-arithmeticbedtools

  R

  •

  Other

  •24•94•0•0•Updated Jan 11, 2026Jan 11, 2026

• remote-ssh-positron

  Public
  Set up Alpine to use Positron

  Shell

  •0•2•0•0•Updated Jan 7, 2026Jan 7, 2026

• squiggy-positron

  Public
  Positron extension to visualize POD5 nanopore signals

  visualizationapinanopore+ 2positronsquiggle

  TypeScript

  •

  MIT License

  •0•0•18•5•Updated Jan 6, 2026Jan 6, 2026

• fcount-rs

  Public
  Rust-based exon counting optimized for RNA-seq

  rna-seqfeaturecounts

  Rust

  •

  MIT License

  •0•0•2•1•Updated Jan 4, 2026Jan 4, 2026

• charmer-rs

  Public
  TUI to monitor snakemake pipelines

  snakemakesnakemake-pipeline

  Rust

  •

  MIT License

  •0•0•0•2•Updated Jan 1, 2026Jan 1, 2026

• cpp11bigwig

  Public
  Read bigWig and bigBed files in R

  C

  •

  Other

  •1•3•0•0•Updated Dec 11, 2025Dec 11, 2025

• hesselberthlab.org

  Public
  Lab website

  HTML

  •

  MIT License

  •0•0•0•1•Updated Dec 7, 2025Dec 7, 2025

• morrison-chronic-chikv

  Public
  Quantification of CHIKV RNA at 28 dpi using scRNA-seq

  HTML

  •0•1•0•0•Updated Nov 11, 2025Nov 11, 2025

• morrison-chronic-chikv-xenium

  Public
  Quantification of CHIKV RNA at 28 dpi using spatial transcriptomics

  R

  •0•1•0•0•Updated Oct 24, 2025Oct 24, 2025

• molb-7950

  Public
  MOLB 7950: Informatics and Statistics for Molecular Biology

  HTML

  •0•4•9•1•Updated Oct 20, 2025Oct 20, 2025

• aa-tRNA-seq

  Public
  Public-facing repo for aa-tRNA-seq pre-print

  Python

  •0•2•0•0•Updated Oct 8, 2025Oct 8, 2025

• remora

  Public
  Methylation/modified base calling separated from basecalling.

  Python

  •

  Other

  •25•0•0•0•Updated Aug 20, 2025Aug 20, 2025

• pneuro-onc-browsers

  Public
  Pediatric Neuro-oncology Cell Atlas

  TeX

  •

  MIT License

  •0•0•1•0•Updated Aug 11, 2025Aug 11, 2025

• raer

  Public
  Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments

  rna-seq-analysissingle-cell-rna-seqbioconductor-package+ 1single-cell-analysis

  C

  •

  Other

  •2•10•2•0•Updated Jul 15, 2025Jul 15, 2025

• antigen-exchange-xenium

  Public
  Xenium analysis for Sheridan et al.

  R

  •0•0•0•0•Updated Jul 13, 2025Jul 13, 2025

• antigen-exchange

  Public
  Analysis for Sheridan et al.

  R

  •0•0•0•0•Updated Jul 13, 2025Jul 13, 2025

• scraps

  Public
  Single-cell RNA Processing Software

  Python

  •

  MIT License

  •4•11•7•0•Updated Jun 17, 2025Jun 17, 2025

• purrr

  Public
  A functional programming toolkit for R

  R

  •

  Other

  •293•0•0•0•Updated Jun 6, 2025Jun 6, 2025

• yeastgenes

  Public
  R data package for yeast gene expression

  R

  •

  Other

  •0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

• clustifyr

  Public
  Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets

  rna-seqclustersmarker-genes+ 2single-cell-rna-seqassign-identities

  R

  •

  MIT License

  •15•126•0•0•Updated Apr 16, 2025Apr 16, 2025

• aa-tRNA-seq-analysis-template

  Public
  Quarto template for aa-tRNA-seq anaysis

  rna-seq-analysisquarto-template

  R

  •

  MIT License

  •0•0•0•0•Updated Mar 21, 2025Mar 21, 2025

• nihexporter

  Public
  An R data package for NIH EXPORTER data

  spendinggrantsnih

  R

  •

  Other

  •13•15•1•0•Updated Mar 8, 2025Mar 8, 2025

• modkit

  Public
  A bioinformatics tool for working with modified bases

  Rust

  •

  Other

  •21•0•0•0•Updated Mar 6, 2025Mar 6, 2025

• squigualiser

  Public
  Visualise and analyse nanopore (ONT) raw signals

  Python

  •

  MIT License

  •4•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• WarpDemuX

  Public
  direct RNA nanopore sequencing barcode design and demultiplexing

  Jupyter Notebook

  •

  Other

  •5•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• rbitemplate

  Public
  RBI pkgdown template

  R

  •

  Other

  •0•0•1•0•Updated Jan 12, 2025Jan 12, 2025