jdblischak/2014-09-18-chicago

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jdblischak/2014-09-18-chicago

jdblischak

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Software Carpentry bootcamp at University of Chicago

singleCellSeq

Batch effects and the effective design of single-cell gene expression studies

smk-simple-slurm

A simple Snakemake profile for Slurm without --cluster-config

r-project-workflows

List of workflow tools for R projects

git-for-science

A quick introduction to version control with Git and GitHub

reproducible-research-ctv

**Archived** CRAN Task View: Reproducible Research

singlecell-qtl

Discovery and characterization of variance QTLs in human induced pluripotent stem cells

tbd

To be determined... -> TB Dissertation

fucci-seq

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis

ctv-project-workflows

R Task View: Project Workflows

cardioqtl

faviconPlease

Find URL for a website's favicon

workflowrBeta

The beta release of workflowr

giladlab-midway-guide

Guide to using RCC Midway

repdoc

Package for testing workflowr features

filter_probes

Filter Illumina HT-12 v4 probes for presence of HapMap CEU SNPs

tb-suscept

Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells

jdb-conda

Scripts, recipes, and docs for maintaining Conda packages

Jupyter Notebook

2016-09-15-chicago

Website for 2016 Software Carpentry workshop for UChicago BSD

r-intermediate-altmetrics

A 2-day workshop on intermediate-level programming with R

ci4r

Demonstrate CI testing for an R package

midway-subread-pipeline

Process RNA-seq data with Subread on RCC Midway

2016-09-14-introR

Website for 2016 UChicago BSD Introduction to R Workshop

blog.jdblischak.com

whereami

Visualize your current working directory

computing-tips

Computing tips for scientists

dsc-mouthwash

Dynamic Statistical Comparisons for MOUTHWASH simulations

test-issue-templates

Temporary repo to test GitHub Issue Templates

open-sci-template

Template for creating project website. Facilitates open science. Powered by R, knitr, and pandoc.

swc-novice-r

Data files for teaching Software Carpentry novice R lessons

dc-bioc-limma

DataCamp: Differential expression analysis in R with limma

workflowr-demo01

An example site created with workflowr

r-reproducibility-challenge

Exercise on reproducible research with R