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    48 repositories

    • Ambilogue

      Public
      Compare methods that address ambient RNA contamination with the Ambilogue.
      comparisonsingle-cellcontamination
      comparisonsingle-cellcontaminationambient-rna
      HTML
      •0•0•0•0•Updated Oct 20, 2026Oct 20, 2026

    • JAFFA

      Public
      JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
      C++
      •
      Other
      •23•119•20•1•Updated Oct 19, 2026Oct 19, 2026

    • doublet-ambient-paper

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 11, 2026Oct 11, 2026

    • flex-fusion-probes

      Public
      Closing the fusion-detection gap in single-cell RNA-seq with a scalable, probe-based workflow
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 31, 2026Aug 31, 2026

    • Damsel

      Public
      R
      •
      Other
      •0•1•1•0•Updated Aug 25, 2026Aug 25, 2026

    • flexify

      Public
      Automated fusion and non-fusion probe design for the 10x Genomics Flex platform
      R
      •
      MIT License
      •0•4•0•0•Updated Jul 31, 2026Jul 31, 2026

    • barbieQ

      Public
      R
      •
      Other
      •0•1•0•0•Updated Jul 3, 2026Jul 3, 2026

    • barbieQ-paper-analysis

      Public
      R
      •1•0•0•0•Updated Jun 12, 2026Jun 12, 2026

    • TALLSorts

      Public
      TALLSorts is a T-cell acute lymphoblastic leukaemia (T-ALL) subtype classifier, taking gene expression counts and making predictions into 8 subtypes (for now).
      Python
      •
      MIT License
      •1•3•1•0•Updated Jun 5, 2026Jun 5, 2026

    • LemonSplice

      Public
      0•0•0•0•Updated Jun 4, 2026Jun 4, 2026

    • splatter

      Public
      Simple simulation of single-cell RNA sequencing data
      bioinformaticssimulationbioconductor
      bioinformaticssimulationbioconductorscrna-seq
      R
      •
      GNU General Public License v3.0
      •60•234•7•2•Updated May 20, 2026May 20, 2026

    • paediatric-cf-inflammation-citeseq

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 2, 2026Apr 2, 2026

    • MINTIE-paper-analysis

      Public
      Code for generating the figures and analyses presented in the MINTIE paper
      R
      •
      MIT License
      •1•0•0•0•Updated Dec 9, 2025Dec 9, 2025

    • TobleroneWeb

      Public
      Web app incorporating https://github.com/oshlack/toblerone
      JavaScript
      •
      MIT License
      •1•0•0•0•Updated Nov 11, 2025Nov 11, 2025

    • ALLSorts

      Public
      ALLSorts is a B-Cell Acute Lymphoblastic Leukemia (B-ALL) subtype classifier. From gene expression counts to over 18 subtypes.
      Python
      •
      MIT License
      •11•18•6•3•Updated Jul 30, 2025Jul 30, 2025

    • oshlack.github.io

      Public
      Oshlack Lab website
      JavaScript
      •15•2•0•0•Updated Jul 3, 2025Jul 3, 2025

    • flex-doublets

      Public
      TeX
      •
      Other
      •0•1•0•0•Updated Jun 12, 2025Jun 12, 2025

    • missMethyl

      Public
      Bioconductor package for analysis of methylation data from Illumina's Infinium HumanMethylation arrays.
      R
      •6•15•6•0•Updated Mar 3, 2025Mar 3, 2025

    • xenanoseq

      Public
      Nanopore demultiplexing, QC and alignment pipeline for xenograph RNA-seq experiments
      Nextflow
      •
      MIT License
      •109•0•0•0•Updated Jul 24, 2024Jul 24, 2024

    • MINTIE

      Public
      Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.
      rna-seqcancertranscriptomics
      rna-seqcancertranscriptomicsstructural-variationduplicationsrare-diseasegene-fusionscryptic-variants
      Python
      •
      MIT License
      •8•38•2•0•Updated Jul 1, 2024Jul 1, 2024

    • hashtag-demux-paper

      Public
      Analysis code for "Benchmarking single-cell hashtag oligo demultiplexing methods" paper
      R
      •
      Other
      •0•3•0•0•Updated Aug 25, 2023Aug 25, 2023

    • TobleroneApp

      Public
      Desktop app incorporating https://github.com/oshlack/toblerone
      JavaScript
      •
      MIT License
      •1•0•0•0•Updated Jan 24, 2023Jan 24, 2023

    • Toblerone

      Public
      Rust
      •
      MIT License
      •2•6•4•0•Updated Jan 24, 2023Jan 24, 2023

    • Clinker

      Public
      Gene Fusion Visualiser
      Python
      •
      MIT License
      •12•53•16•0•Updated Jan 15, 2023Jan 15, 2023

    • paed-cf-cite-seq

      Public
      R
      •0•3•1•0•Updated Dec 23, 2022Dec 23, 2022

    • methyl-geneset-testing

      Public
      R
      •
      MIT License
      •2•9•1•1•Updated Nov 18, 2022Nov 18, 2022

    • TopDeck

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Oct 21, 2022Oct 21, 2022

    • speckle

      Public
      R package for specialised analysis of single cell data
      R
      •
      GNU General Public License v3.0
      •5•42•9•0•Updated Oct 14, 2022Oct 14, 2022

    • Slinker

      Public
      Slinker offers a succinct and complementary method to visualise RNA-Seq data through superTranscripts.
      Python
      •
      MIT License
      •3•21•5•0•Updated Jun 13, 2022Jun 13, 2022

    • Corset

      Public
      Software for clustering de novo assembled transcripts and counting overlapping reads
      C++
      •
      Other
      •21•80•4•0•Updated Feb 11, 2022Feb 11, 2022
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