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    • rotahost-eqtl

      Public
      RotaHost sc-eQTL + sc-pQTL pipeline following sc-eQTLGen WG3 (Kaptijn et al. 2026)
      WDL
      0000Updated Apr 17, 2026Apr 17, 2026
    • CHRF_2026

      Public
      Computational workshop material for CHRF
      Jupyter Notebook
      4000Updated Apr 1, 2026Apr 1, 2026
    • Scripts and input file for single-cell open reading frame (ORF) barcode extraction from fastq files. These files are associated with the study of LAT mutations …
      Python
      0000Updated Oct 23, 2025Oct 23, 2025
    • cellranger_vdj

      Public
      Minor edit to the cumulus cellranger workflow to enable RNA+VDJ linking
      WDL
      BSD 3-Clause "New" or "Revised" License
      1000Updated Jun 10, 2025Jun 10, 2025
    • Workflow scripts for data analyses of multi-omics data generated using Seq-Well S3
      R
      MIT License
      1100Updated Apr 17, 2025Apr 17, 2025
    • KEMRI_Kilifi_2024_workshop

      Public
      Jupyter Notebook
      4000Updated Sep 24, 2024Sep 24, 2024
    • Jupyter Notebook
      0100Updated Aug 5, 2024Aug 5, 2024
    • Computational workshop material for the HCA thailand training lives here
      Jupyter Notebook
      6300Updated Jul 12, 2024Jul 12, 2024
    • Code for the manuscript: Compressed phenotypic screening empowers scalable biological discovery.
      Jupyter Notebook
      2900Updated Apr 17, 2024Apr 17, 2024
    • mTB_CD8_Depletion

      Public
      Jupyter Notebook
      MIT License
      0100Updated Sep 28, 2023Sep 28, 2023
    • Code and analyses for Mead et al Nature BME 2022
      R
      MIT License
      1300Updated May 23, 2022May 23, 2022
    • Jupyter Notebook
      MIT License
      0200Updated Mar 10, 2022Mar 10, 2022
    • tcrgo

      Public
      Identification and quantification of Seq-Well TCR transcripts and their recovered CDR3 sequences.
      Python
      2150Updated Oct 13, 2021Oct 13, 2021
    • The Alexandria project aims to facilitate single-cell data analysis for users through providing an accessible data repository along with workflows, notebooks, a…
      Jupyter Notebook
      3911Updated Aug 24, 2021Aug 24, 2021
    • Edited SARS-CoV-2 genome fasta and gtf for Ziegler et al. 2021
      0200Updated Feb 10, 2021Feb 10, 2021
    • WDL
      MIT License
      1010Updated Nov 6, 2020Nov 6, 2020
    • Code for Downsampling both FASTQs and BAMs (used in Hughes, Wadsworth, Gierahn et al 2020 to benchmark Seq-Well S^3 and 10x V3)
      1000Updated Jul 20, 2020Jul 20, 2020
    • WDL
      0200Updated May 18, 2020May 18, 2020
    • HowTosRTD

      Public
      The Read The Docs version of our GitHub HowTos wiki.
      0000Updated Mar 19, 2020Mar 19, 2020
    • Our lab's public workflow (WDL) for the mixcr tool (https://mixcr.readthedocs.io/en/master/) authored by the mixcr team
      WDL
      Other
      0000Updated Oct 23, 2019Oct 23, 2019
    • .wdl files for archiving and unarchiving sequencing runs
      WDL
      0000Updated May 22, 2019May 22, 2019
    • This repo is for the metadata schemas associated with the HCA
      Python
      Apache License 2.0
      31000Updated Mar 18, 2019Mar 18, 2019
    • Conner

      Public
      Scripts and the such that might be useful to people
      0000Updated Sep 7, 2018Sep 7, 2018
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