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@DiseaseNeuroGenomics

Center for Disease Neurogenomics @ Mount Sinai

Open source software, documentation and applications for analysis of functional genomics datasets
README.md

Welcome to the open source software repositories developed by the Center for Disease Neurogenomics (CDN) at the Icahn School of Medicine at Mount Sinai located in New York City. We develop statistical methods and software to ask biological questions from the large-scale functional genomics datasets generated by the group and the broader genomics field.

The members of the CDN are commited to developing software that is:

  • Open source
  • Well documented
  • Scalable to large functional genomics datasets
  • Statistically rigorous
  • Reproducible

We emphasize integration with standard practices from R, CRAN and Bioconductor.

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  1. variancePartition variancePartition Public

    Forked from GabrielHoffman/variancePartition

    Quantify and interpret divers of variation in multilevel gene expression experiments

    R 4

  2. decorate decorate Public

    Forked from GabrielHoffman/decorate

    Differential Epigenetic Correlation Test

    R 1

  3. MMQTL MMQTL Public

    Forked from jxzb1988/MMQTL

    MMQTL is a statistical package applying meta-analysis to detect multiple QTL signals integrating signals among conditions, with control for population structure and relatedness

    C++

  4. remaCor remaCor Public

    Forked from GabrielHoffman/remaCor

    remaCor: Random effects meta-analysis for correlated test statistics

    R 1

Repositories

Showing 10 of 25 repositories
  • PsychAD Public
    DiseaseNeuroGenomics/PsychAD’s past year of commit activity
    HTML 0 0 0 0 Updated Nov 8, 2024
  • dreamlet Public Forked from GabrielHoffman/dreamlet

    Perform differential expression analysis on cohort-scale single cell datasets using linear mixed models

    DiseaseNeuroGenomics/dreamlet’s past year of commit activity
    HTML 10 4 1 0 Updated Nov 5, 2024
  • variancePartition Public Forked from GabrielHoffman/variancePartition

    Quantify and interpret divers of variation in multilevel gene expression experiments

    DiseaseNeuroGenomics/variancePartition’s past year of commit activity
    R 4 14 1 0 Updated Nov 5, 2024
  • PsychADxD Public

    PsychAD Cross-Disorder Capstone - Single-cell atlas of transcriptomic vulnerability across multiple neuropsychiatric and neurodegenerative diseases

    DiseaseNeuroGenomics/PsychADxD’s past year of commit activity
    Python 0 0 0 0 Updated Oct 31, 2024
  • snMultiome Public

    Analysis scripts for snMultiome project

    DiseaseNeuroGenomics/snMultiome’s past year of commit activity
    R 0 0 0 0 Updated Oct 25, 2024
  • nps_ad Public

    R code for analysis of PsychAD projects

    DiseaseNeuroGenomics/nps_ad’s past year of commit activity
    R 0 0 0 0 Updated Oct 21, 2024
  • molecular_profiling Public

    Code for Molecular Profiling manuscript

    DiseaseNeuroGenomics/molecular_profiling’s past year of commit activity
    R 0 MIT 0 0 0 Updated Sep 26, 2024
  • PsychAD_snTWAS Public Forked from svenkatesh25/PsychAD_snTWAS

    Repository for data associated with the psychAD snTWAS paper. Synapse information located at https://www.synapse.org/Synapse:syn63181047/files/

    DiseaseNeuroGenomics/PsychAD_snTWAS’s past year of commit activity
    0 1 0 0 Updated Sep 16, 2024
  • crumblr Public Forked from GabrielHoffman/crumblr

    Count ratio uncertainty modeling base linear regression

    DiseaseNeuroGenomics/crumblr’s past year of commit activity
    R 1 1 0 0 Updated Jul 16, 2024
  • psychAD_SciData Public Forked from pnm27/psychAD_SciData

    Plot figures from the psychAD paper

    DiseaseNeuroGenomics/psychAD_SciData’s past year of commit activity
    Jupyter Notebook 0 MIT 1 0 0 Updated Jun 12, 2024
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