Allen Institute for Immunology

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44 repositories

sound-life-scrna-analysis
Public
Annotation and Analysis of 13M cells from the Sound Life Cohort
Jupyter Notebook
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Other
•0•0•0•0•Updated Aug 16, 2025Aug 16, 2025
ALTRA-manuscript
Public
repository for codes to generate figures for ALTRA manuscript
flow manuscript scrna olink
Jupyter Notebook
•0•2•0•0•Updated Aug 15, 2025Aug 15, 2025
H5weaver
Public
R functions for reading, rearranging, and writing HDF5 files with 10x-compatible structure
r pipeline rmarkdown hdf5 transcriptomics
R
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Other
•0•1•2•1•Updated Jul 25, 2025Jul 25, 2025
IHA-Figure
Public
immunology aging vaccination
Jupyter Notebook
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Other
•0•0•0•0•Updated Jul 21, 2025Jul 21, 2025
spatial_tls_manuscript
Public
Spatial transcriptomics analysis for Bangs et al., 2025
manuscript xenium
Jupyter Notebook
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Other
•0•0•0•0•Updated Jul 11, 2025Jul 11, 2025
aifi-healthy-pbmc-reference
Public
Assembly and Annotation of the Human Immune Health Atlas
Jupyter Notebook
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Other
•1•6•0•0•Updated Jun 10, 2025Jun 10, 2025
Xenium-Benchmarking-Gill
Public
Jupyter Notebook
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GNU General Public License v3.0
•0•1•0•0•Updated Jun 4, 2025Jun 4, 2025
pediatric_IH
Public
Repo for all pediatric immune health code
0•0•0•0•Updated Jun 3, 2025Jun 3, 2025
batchreporter
Public
pipeline
HTML
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Other
•0•1•0•0•Updated May 9, 2025May 9, 2025
MOCHA
Public template
R package for single-cell Open Chromatin Identification & Downstream Analysis
R
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GNU General Public License v3.0
•0•2•12•2•Updated Apr 2, 2025Apr 2, 2025
MATCHA
Public
Modeling Associations for all The Creative, Heterogeneous Assays
R
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GNU General Public License v3.0
•0•0•0•0•Updated Mar 15, 2025Mar 15, 2025
ArchR
Public
ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
R
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MIT License
•150•1•0•1•Updated Mar 4, 2025Mar 4, 2025
SPARROW
Public
Jupyter Notebook
•2•1•0•0•Updated Dec 3, 2024Dec 3, 2024
cell-hashing-pipeline
Public
Processing of scRNA-seq cell hashing data
docker wrapper r pipeline transcriptomics cell-hashing
R
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Other
•0•1•0•0•Updated Oct 29, 2024Oct 29, 2024
CryoSCAPE
Public
Jupyter Notebook
•0•1•0•0•Updated Sep 5, 2024Sep 5, 2024
ATAComb
Public
Functions for QC and analysis of ATAC-seq data
r pipeline atac
R
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Other
•0•0•0•0•Updated Aug 17, 2024Aug 17, 2024
SeuratLabeler
Public
R package for bundling Seurat Label Transfer objects, markdowns, and functions
r pipeline labeling transcriptomics seurat
R
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Other
•0•1•0•1•Updated Aug 9, 2024Aug 9, 2024
HTOparser
Public
R functions for parsing cell hashing data
r pipeline rmarkdown transcriptomics scrna cell-hashing fiveprime
R
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Other
•0•1•0•0•Updated Aug 9, 2024Aug 9, 2024
tenx-rnaseq-pipeline
Public
Pipeline scripts for processing 10x Genomics scRNA-seq data
metadata wrapper r pipeline transcriptomics tenxgenomics scrna
R
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Other
•0•1•0•0•Updated Aug 9, 2024Aug 9, 2024
epiAneufinder
Public
R package to detect breakpoints and assign somies to scATAC-seq data
HTML
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GNU General Public License v3.0
•9•0•0•0•Updated Aug 2, 2024Aug 2, 2024
certpro-workflow-demos
Public
Demonstration notebooks for HISE Certificate of Reproducibility workflows
Jupyter Notebook
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Other
•0•0•0•0•Updated Jul 11, 2024Jul 11, 2024
MOCHA_Manuscript
Public
Repository to include Figure Generations for MOCHA
R
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GNU General Public License v3.0
•0•0•0•0•Updated Jun 21, 2024Jun 21, 2024
repro-vrd-tea-seq-common
Public
Common files used for analysis of VRd TEA-seq data
0•0•0•0•Updated Apr 29, 2024Apr 29, 2024
repro-vrd-tea-seq
Public
Reproducible analysis of T cell VRd treatment TEA-seq
Jupyter Notebook
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Other
•0•1•1•0•Updated Apr 29, 2024Apr 29, 2024
serverless-registry-proxy
Public
Serverless reverse proxy for exposing container registries (GCR, Docker Hub, Artifact Registry etc) on custom domains.
Go
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Apache License 2.0
•60•0•0•1•Updated Mar 13, 2024Mar 13, 2024
multicelltypist
Public
A tool for semi-automatic cell type classification
Python
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MIT License
•48•0•0•0•Updated Mar 8, 2024Mar 8, 2024
fake_hisepy
Public
placeholder project for HISE Python SDK
Python
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MIT License
•0•0•0•0•Updated Feb 11, 2024Feb 11, 2024
scrubleta
Public
A fork of Scrublet that uses Actual cell-hashing-derived doublets
Jupyter Notebook
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MIT License
•74•0•0•0•Updated Jan 27, 2024Jan 27, 2024
repro-vrd-tea-seq-deg-app
Public
tea
Jupyter Notebook
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Other
•0•0•0•0•Updated Jan 5, 2024Jan 5, 2024
gke-shift-left-cost
Public
Fork of google's costing lib
Go
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Apache License 2.0
•9•0•0•0•Updated Dec 14, 2023Dec 14, 2023