Pinned Repositories
CellaRepertorium
Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)
CoordinatedMicrobiome
Analysis for "Neonatal gut and respiratory microbiota: coordinated development through time and space"
CoordinatedTCellsMicrobiota
Code and data for "Aberrant newborn T cell and microbiota developmental trajectories predict respiratory compromise during infancy"
Genesee
Core functions for genomics project templating
HurdleNormal
Estimation and sampling for multi-dimensional Hurdle models on a Normal density with applications to single-cell co-expression
NR4A-RA-B-cells
Data, scripts and intermediate outputs supporting "Dynamic spectrum of ectopic lymphoid B cell activation in the RA synovium characterized by NR4A nuclear receptor expression"
RA-BCell-Response
Data and scripts supporting "T Cell–Dependent Affinity Maturation and Innate Immune Pathways Differentially Drive Autoreactive B Cell Responses in Rheumatoid Arthritis" by Lu, et al 2018
RNASeqPipelineR
Streamline the processing of RNASeq data
Zeisel2015Data
Packaged data from Zeisel (2015)
MAST
Tools and methods for analysis of single cell assay data in R
amcdavid's Repositories
amcdavid/CellaRepertorium
Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)
amcdavid/HurdleNormal
Estimation and sampling for multi-dimensional Hurdle models on a Normal density with applications to single-cell co-expression
amcdavid/CoordinatedMicrobiome
Analysis for "Neonatal gut and respiratory microbiota: coordinated development through time and space"
amcdavid/CoordinatedTCellsMicrobiota
Code and data for "Aberrant newborn T cell and microbiota developmental trajectories predict respiratory compromise during infancy"
amcdavid/RA-BCell-Response
Data and scripts supporting "T Cell–Dependent Affinity Maturation and Innate Immune Pathways Differentially Drive Autoreactive B Cell Responses in Rheumatoid Arthritis" by Lu, et al 2018
amcdavid/Genesee
Core functions for genomics project templating
amcdavid/NR4A-RA-B-cells
Data, scripts and intermediate outputs supporting "Dynamic spectrum of ectopic lymphoid B cell activation in the RA synovium characterized by NR4A nuclear receptor expression"
amcdavid/amcdavid.github.io
Website derived from http://scotte.github.io/jekyll-clean
amcdavid/AMmisc
Miscellaneous R functions mainly for interactive use
amcdavid/biobroom
Tidy up computational biology objects
amcdavid/BioC2023
amcdavid/BuildABiocWorkshop
Template for building a bioconductor workshop package using github actions
amcdavid/clusterProfiler
:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters
amcdavid/DropletUtils
Clone of the Bioconductor repository for the DropletUtils package.
amcdavid/fasta-genomes-alignments-bioc
A short tutorial on using Bioconductor resources for genomic annotation, illustrated using SARS-CoV-2 sequencing
amcdavid/flowStats
flowStats: algorithms for flow cytometry data analysis using BioConductor tools
amcdavid/GeneseeBulk
Pipeline, analysis functions and markdown templates for bulk RNAseq
amcdavid/Hackathon
Automated scoring of data contests using R and github
amcdavid/Hackathon-432-2020
amcdavid/Hackathon-Summer-2020
Data and details for University of Rochester Biomedical Data Science Hackathon
amcdavid/hw02-accidents
amcdavid/lab04-laquinta-dos
More spatial data wrangling and joins
amcdavid/LintMarkdown
Lint R and Rmd with default styles
amcdavid/rnoaa
R interface to many NOAA data APIs
amcdavid/rvcheck
:white_check_mark:R/Package Version Check
amcdavid/scDblFinder
Methods for detecting doublets in single-cell RNAseq data
amcdavid/scRNA-tools
Table of software for the analysis of single-cell RNA-seq data.
amcdavid/seurat
R toolkit for single cell genomics
amcdavid/symphony
Efficient and precise single-cell reference atlas mapping with Symphony
amcdavid/ZeroInflatedMM
Multi-level models and simulations for zero-inflated data