Raychaudhuri Lab

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69 repositories

starCAT_website
Public
HTML
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GNU General Public License v3.0
•0•0•0•0•Updated Nov 7, 2025Nov 7, 2025
symphony
Public
Efficient and precise single-cell reference atlas mapping with Symphony
r mapping scrna-seq bioinfo
Jupyter Notebook
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GNU General Public License v3.0
•23•111•17•0•Updated Oct 31, 2025Oct 31, 2025
harmony
Public
Fast, sensitive and accurate integration of single-cell data with Harmony
algorithm r scrna-seq data-integration
R
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Other
•104•603•80•2•Updated Oct 10, 2025Oct 10, 2025
TCAT_analysis
Public
Code repository for TCAT analyses
Jupyter Notebook
•2•11•0•0•Updated Sep 26, 2025Sep 26, 2025
starCAT
Public
Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs
Jupyter Notebook
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MIT License
•3•80•6•1•Updated Sep 19, 2025Sep 19, 2025
AMP_SLE_Kidney
Public
Scripts for AMP_SLE_Kidney
Jupyter Notebook
•0•0•0•0•Updated Sep 9, 2025Sep 9, 2025
cna
Public
Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.
python single-cell
Python
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GNU General Public License v3.0
•5•56•0•0•Updated Jun 1, 2025Jun 1, 2025
craft-seq
Public
Code for analysis of CRAFT-seq data
Jupyter Notebook
•0•2•0•0•Updated May 15, 2025May 15, 2025
GeNA-applied
Public
Code and analyses supporting the GeNA single-cell csaQTL manuscript.
Jupyter Notebook
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GNU General Public License v3.0
•0•2•0•0•Updated Apr 29, 2025Apr 29, 2025
cna-display
Public
Generation of display items for CNA paper
Jupyter Notebook
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MIT License
•1•3•0•0•Updated Apr 28, 2025Apr 28, 2025
cna-sim
Public
Simulation code for CNA evaluation
Python
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GNU General Public License v3.0
•0•0•1•0•Updated Apr 28, 2025Apr 28, 2025
SCENT
Public
Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA
R
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Other
•10•77•1•0•Updated Apr 21, 2025Apr 21, 2025
snATAC_benchmark
Public
Code corresponding to Weinand et al., Defining effective strategies to integrate multi-sample single-nucleus ATAC-seq datasets via a multimodal-guided approach, Submitted.
Jupyter Notebook
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GNU General Public License v3.0
•1•1•0•0•Updated Apr 8, 2025Apr 8, 2025
amp_phase1_ra
Public
🌾 Zhang, et al, Nature Immunology, 2019. Use single-cell transcriptomics and proteomics to study autoimmune diseases.
r jupyter-notebook autoimmune single-cell-genomics single-cell-proteomics immunogenomics
Jupyter Notebook
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GNU General Public License v3.0
•13•20•1•0•Updated Mar 11, 2025Mar 11, 2025
EarlyLate_RNA_eQTL
Public
R
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GNU General Public License v3.0
•0•0•0•0•Updated Feb 18, 2025Feb 18, 2025
TiRP
Public
code repository for Lagattuta et al. "Repertoire analyses reveal T cell receptor sequence features that influence T cell fate." Nat. Imm. (2022)
tcr single-cell sequence-analysis mixed-effects-models treg
Jupyter Notebook
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GNU General Public License v3.0
•5•13•1•0•Updated Jan 28, 2025Jan 28, 2025
crescendo
Public
Crescendo for single-gene correction in single-cell RNA-sequencing data
R
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Other
•1•5•2•0•Updated Dec 10, 2024Dec 10, 2024
tcrpheno_analysis
Public
Code for analysis of TCR and T cell state data in Lagattuta, et al. Cell Reports 2025
R
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MIT License
•1•0•0•0•Updated Nov 24, 2024Nov 24, 2024
presto
Public
Fast Wilcoxon and auROC
Jupyter Notebook
•35•194•17•1•Updated Nov 8, 2024Nov 8, 2024
HLA_analyses_tutorial
Public
A thorough tutorial on HLA imputation and association, accompanying our manuscript "Tutorial: A statistical genetics guide to identifying HLA alleles driving complex disease"
Jupyter Notebook
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GNU General Public License v3.0
•12•70•0•0•Updated Oct 10, 2024Oct 10, 2024
GeNA
Public
Genotype-Neighborhood Associations: A tool for identifying genetic variant associations to the abundance of cell states in single-cell datasets
Jupyter Notebook
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GNU General Public License v3.0
•1•14•0•0•Updated Oct 5, 2024Oct 5, 2024
singlecellmethods
Public
Collection of useful methods for single cell analysis
Jupyter Notebook
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GNU General Public License v3.0
•5•14•1•0•Updated Aug 22, 2024Aug 22, 2024
RA_ATAC_multiome
Public
Code corresponding to Weinand et al., The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis, Nature Communications, 2024
Jupyter Notebook
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GNU General Public License v3.0
•1•2•0•0•Updated Jun 24, 2024Jun 24, 2024
IMPACT
Public
Code for creating cell-type-specific regulatory element annotation files
R
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GNU General Public License v3.0
•8•18•1•2•Updated Jun 11, 2024Jun 11, 2024
TB-g2g
Public
Code for genome-to-genome study of tuberculosis
Jupyter Notebook
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GNU General Public License v3.0
•1•0•0•0•Updated May 20, 2024May 20, 2024
PAUSE_eQTL
Public
Code for dynamic eQTL analysis of PAUSE trial
R
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GNU General Public License v3.0
•1•1•0•0•Updated Mar 20, 2024Mar 20, 2024
reQTL
Public
Mapping of response eQTL in single cells
R
•0•2•0•0•Updated Mar 8, 2024Mar 8, 2024
RA_Atlas_CITEseq
Public
RA Synovial Single-cell Multimodal Cell Atlas
Jupyter Notebook
•3•18•1•0•Updated Mar 6, 2024Mar 6, 2024
scHLApers
Public
Code to run the scHLApers pipeline for personalized single-cell HLA quantification
expression alignment single-cell hla
Jupyter Notebook
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GNU General Public License v3.0
•1•17•1•0•Updated Jan 10, 2024Jan 10, 2024
HLA-TAPAS
Public
HLA-TAPAS pipeline for HLA association and fine-mapping studies
Jupyter Notebook
•24•54•17•1•Updated Dec 19, 2023Dec 19, 2023