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20240310_mpra_analysis

alveolar_macrophage_subsets_ards

Code repository for Morell et al. study of BAL in ARDS and non-ARDS intubated patients.

annotables

R data package for annotating/converting Gene IDs

bajzik_et_al_ar101oraldesensitizationtherapy

Analysis code for the Wambre lab manuscript, "Ar101 Oral Desensitization Therapy for Peanut Allergy Induces Dynamic Changes in Peanut-Specific Immune Responses"

bioinformaticschallengecourse2022

Repository for storing information and data from the Bioinformatics 2022 Autumn Challenge Course

bridiscovr

Distribution analysis across clusters of a parent population overlaid with a rare subpopulation (DISCOV-R)

bripipetools

tools for managing genomics pipelines at BRI

brirutils

BRI R language Utilities for data processing

buckner_linsley_cit-specific

countsubsetnorm

Helper functions to conduct subsetting and normalization of RNAseq data. Most of them are wrappers to facilitate workflows.

cpeptidetools

R package with functions for handling C-peptide data from MMTTs and OGTTs

data_carpentry_workshop_2022

Repository to hold code for the 2022 Intro to R Data Carpentry workshop hosted by the BRI Bioinformatics Team

data_carpentry_workshop_2024

R coding bootcamp for Researchers are BRI

datasharing

The Leek group guide to data sharing

dgetools

Differential Gene Expression Analysis Tools

diggins_serti_linsley_jci_insight_2020

Code and data for JCI Insight publication "Exhausted-like CD8 T cell phenotypes linked to C-peptide preservation in alefacept-treated T1D subjects"

galaxyconfig

genesettools

Accessory tools to facilitate gene set analyses of RNAseq data.

germline-like-tcr-alpha-chains-shared-between-autoreactive-t-cells-in-blood-and-pancreas

gxbrowser

BRI Gene Browser for integrating Microarray, RNA-seq data, expression data with demographic and clinical information

gxrscripts

R Scripts required for Gene Expression Browser (gxbrowser)

islet-autoreactive-cd4-t-cells-are-linked-with-response-to-alefacept-in-type-1-diabetes

johnpray_bach2_variant_tcells

Code repository for the manuscript "Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells" from the Ray lab

kubespray

Deploy a Production Ready Kubernetes Cluster

limmatools

Accessory functions for differential gene expression analyses using limma

masttools

Helper utilities for using the single-cell RNA-seq analysis package MAST

mischelpers

Miscellaneous helper functions for common tasks. A hodgepodge of stuff that doesn't fit into other packages.

muppits1modules

ICAC3 Pediatric Asthma MUPPITS 1 Modules, Voom, and Design Data Package

netr

Tools for network analysis

oralmucosa_woodward_davis_and_prlic_analysis

Code for the publication: A human TH17 population with a tissue-resident signature in healthy and inflamed mucosal tissues