daskelly Goto Github PK

academic_website2

Personal website of Dan Skelly

ase

repo for code to implement allele-specific gene expression model of Skelly et al. 2011 Genome Res https://dx.doi.org/10.1101/gr.119784.110

bam_sampling_utils

Utilities for sampling from BAM files. Focused on 10X CellRanger BAMs.

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

cells_server

repo for setting up a VM to host scRNA-Seq data

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

condor-examples

Example scripts for working with the condor job submission system

das

My personal R package

earlycross

A package containing useful functions for extending the Seurat (https://satijalab.org/seurat/) package for single cell RNA-Seq analysis

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

phb_paper

repo for code to implement private haplotype barcoding

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

single_cell_emase

single_cell_rnaseq

repo for scRNA-Seq code

torque-examples

who_data_obesity

yeast100genomes

repository for data from the _Saccharomyces cerevisiae_ 100 genomes project, http://dx.doi.org/10.1101/gr.185538.114