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    23 repositories

    • rotahost-eqtl

      Public
      RotaHost sc-eQTL + sc-pQTL pipeline following sc-eQTLGen WG3 (Kaptijn et al. 2026)
      WDL
      •0•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • CHRF_2026

      Public
      Computational workshop material for CHRF
      Jupyter Notebook
      •4•0•0•0•Updated Apr 1, 2026Apr 1, 2026

    • Perturb-LAT

      Public
      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
      •0•0•0•0•Updated 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
      •1•0•0•0•Updated Jun 10, 2025Jun 10, 2025

    • MultiOmics_SeqWellS3

      Public
      Workflow scripts for data analyses of multi-omics data generated using Seq-Well S3
      R
      •
      MIT License
      •1•1•0•0•Updated Apr 17, 2025Apr 17, 2025

    • KEMRI_Kilifi_2024_workshop

      Public
      Jupyter Notebook
      •4•0•0•0•Updated Sep 24, 2024Sep 24, 2024

    • MISTI_Bogota_2024_workshop

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Aug 5, 2024Aug 5, 2024

    • HCA_Thailand_2024_workshop

      Public
      Computational workshop material for the HCA thailand training lives here
      Jupyter Notebook
      •6•3•0•0•Updated Jul 12, 2024Jul 12, 2024

    • compressed_screening

      Public
      Code for the manuscript: Compressed phenotypic screening empowers scalable biological discovery.
      Jupyter Notebook
      •2•9•0•0•Updated Apr 17, 2024Apr 17, 2024

    • mTB_CD8_Depletion

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Sep 28, 2023Sep 28, 2023

    • Mead_et_al_NatBME_2021

      Public
      Code and analyses for Mead et al Nature BME 2022
      R
      •
      MIT License
      •1•3•0•0•Updated May 23, 2022May 23, 2022

    • MIT_Milk_Study

      Public
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Mar 10, 2022Mar 10, 2022

    • tcrgo

      Public
      Identification and quantification of Seq-Well TCR transcripts and their recovered CDR3 sequences.
      tcrsingle-cellsingle-cell-rna-seq
      tcrsingle-cellsingle-cell-rna-seqcdr3seq-well
      Python
      •2•1•5•0•Updated Oct 13, 2021Oct 13, 2021

    • alexandria

      Public
      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
      •3•9•1•1•Updated Aug 24, 2021Aug 24, 2021

    • SARSCoV2-genome-reference

      Public
      Edited SARS-CoV-2 genome fasta and gtf for Ziegler et al. 2021
      0•2•0•0•Updated Feb 10, 2021Feb 10, 2021

    • ampliconBCR

      Public
      WDL
      •
      MIT License
      •1•0•1•0•Updated Nov 6, 2020Nov 6, 2020

    • Downsampling-FASTQs-and-BAMs

      Public
      Code for Downsampling both FASTQs and BAMs (used in Hughes, Wadsworth, Gierahn et al 2020 to benchmark Seq-Well S^3 and 10x V3)
      1•0•0•0•Updated Jul 20, 2020Jul 20, 2020

    • kallisto-bustools_workflow

      Public
      WDL
      •0•2•0•0•Updated May 18, 2020May 18, 2020

    • HowTosRTD

      Public
      The Read The Docs version of our GitHub HowTos wiki.
      0•0•0•0•Updated Mar 19, 2020Mar 19, 2020

    • mixcr_workflow

      Public
      Our lab's public workflow (WDL) for the mixcr tool (https://mixcr.readthedocs.io/en/master/) authored by the mixcr team
      WDL
      •
      Other
      •0•0•0•0•Updated Oct 23, 2019Oct 23, 2019

    • archiving-pipeline

      Public
      .wdl files for archiving and unarchiving sequencing runs
      WDL
      •0•0•0•0•Updated May 22, 2019May 22, 2019

    • alexandria-metadata-schema

      Public
      This repo is for the metadata schemas associated with the HCA
      Python
      •
      Apache License 2.0
      •31•0•0•0•Updated Mar 18, 2019Mar 18, 2019

    • Conner

      Public
      Scripts and the such that might be useful to people
      0•0•0•0•Updated Sep 7, 2018Sep 7, 2018
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