Dan Skelly's repositories
CellReports_2018_heart_scRNAseq
data for study of gene expression of non-myocytes in the heart, Skelly et al. 2018 Cell Reports http://dx.doi.org/10.1016/j.celrep.2017.12.072
earlycross
A package containing useful functions for extending the Seurat (https://satijalab.org/seurat/) package for single cell RNA-Seq analysis
single_cell_RNAseq
repo for scRNA-Seq code
CellStemCell_2020_diverse_mESCs
repo accompanying Skelly et al. (2020) Cell Stem Cell
Circulation_2020_heart_AngII
data for study of heart gene expression in chronic stress, McLellan and Skelly et al. 2020 Circulation https://doi.org/10.1161/CIRCULATIONAHA.119.045115
yeast100genomes
repository for data from the _Saccharomyces cerevisiae_ 100 genomes project, http://dx.doi.org/10.1101/gr.185538.114
academic_website2
Personal website of Dan Skelly
bam_sampling_utils
Utilities for sampling from BAM files. Focused on 10X CellRanger BAMs.
cells_server
repo for setting up a VM to host scRNA-Seq data
condor-examples
Example scripts for working with the condor job submission system
das
My personal R package
emase
Expectation-Maximization algorithm for Allele-Specific Expression
enrichR
An R interface to enrichR
example-models
Example models for Stan
fstprobs
experimental package combining fst files with large 3D genotype probability matrices. Note: Not very useful, doesn't lead to significant speedup!
GEMMA
Genome-wide Efficient Mixed Model Association
hg2mm
Small R package to convert between human and mouse gene orthologs
latex-template
Simple repo for storing common files used in LaTeX docs
mouse_scRNAseq
List of mouse scRNA-Seq studies
mytemplates
Test of creating a custom Rmd template
notes
short vignettes for compute tasks I need to refresh occasionally
ProFAT
fork of PerocchiLab/ProFAT
qtl2scan
R/qtl2 module for QTL analysis, including genome scans
reference_traits
Walkthrough for reference traits method
scater
Single cell analysis tools for expression from RNA-seq in R