John Blischak

Login: jdblischak

Company: null

Location: null

Bio: null

Blog: https://bitbucket.org/jdblischak

Blog: https://bitbucket.org/jdblischak

Member of

1. Software Carpentry

Repositories

2013-09-19-chicago

Material for the Software Carpentry boot camp at the University of Chicago Sep. 19-20, 2013

2013-10-03-pasteur

Instructional material for Software Carpentry boot camp at Institut Pasteur.

2013-10-17-uic

Boot camp website and lesson materials for UIC on October 17-18, 2013.

2014-09-18-chicago

Software Carpentry bootcamp at University of Chicago

2014-11-06-fmv

Bootcamp at Faculté de médecine vétérinaire, Université de Montréal, November 2014

2015-04-17-nw

Software Carpentry Workshop at Northwestern University

2015-09-15-chicago

null

2016-09-14-introR

Website for 2016 UChicago BSD Introduction to R Workshop

2016-09-15-chicago

Website for 2016 Software Carpentry workshop for UChicago BSD

2017-09-23-chicago

null

adv-r

Advanced R programming: a book

BackSPIN

Biclustering algorithm

bc

Template for Software Carpentry bootcamp site repository.

Bee_Clustering_Website

null

bioconda-recipes

Conda recipes for the bioconda channel.

bioconda-utils

Utilities for building and managing bioconda recipes

Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

boot-camps

Software Carpentry boot camp material

cardioqtl

null

conda-build

Commands and tools for building conda packages

conda-forge.github.io

Documentation for conda-forge

conda-forge-pinning-feedstock

A conda-smithy repository for conda-forge-pinning.

conda_r_skeleton_helper

Cleaning up Conda r-packages

conda-smithy

The tool for managing conda-forge feedstocks.

conflict-challenge

For challenge at 2015-04-17-nw workshop.

dc-bioc-limma

Differential expression analysis with limma

devtools

Tools to make an R developer's life easier

dox

null

filter_probes

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

fucci-seq

null

giladlab-midway-guide

Guide to using RCC Midway

git2r

R bindings to the libgit2 library

git-for-science

A quick introduction to version control with Git and GitHub

grokking_algorithms

Code for the book Grokking Algorithms (http://manning.com/bhargava)

hutt_ipsc

Mapping eQTLs with GEMMA in 73 Hutterite iPSCs

jdb-conda

Scripts, recipes, and docs for maintaining Conda packages

kallisto

Near-optimal RNA-Seq quantification

ldsc

LD Score Regression (LDSC)

live-demo

null

midway-subread-pipeline

Process RNA-seq data with Subread on RCC Midway

new-project

null

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

nw

null

open-sci-template

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

Phospilot

MSB phosphopilot workups

planets

null

plos_altmetrics_study

What can social media tell us about an article's impact?

r3cr-reproducibility-challenge

Exercise for UChicago BSD course on reproducible research

r-anomalydetection-feedstock

A conda-smithy repository for r-anomalydetection.

r-automap-feedstock

A conda-smithy repository for r-automap.

r-base-feedstock

A conda-smithy repository for r-base.

r-bestglm-feedstock

A conda-smithy repository for r-bestglm.

r-copula-feedstock

A conda-smithy repository for r-copula.

remotes

Install R packages from GitHub, Bitbucket, git, svn repositories, URLs

repdoc

Package for testing workflowr features

r-flexmix-feedstock

A conda-smithy repository for r-flexmix.

r-git2r-feedstock

A conda-smithy repository for r-git2r.

r-haplo.stats-feedstock

A conda-smithy repository for r-haplo.stats.

r-intermediate-altmetrics

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

rmarkdown

Dynamic Documents for R

rmarkdowntown

A Rmd hack. Probably don't use this

rmarkdown-website-envs

R Markdown doesn't knit each file in separate environments when building websites :sadface:

r-nhmmfdr-feedstock

A conda-smithy repository for r-nhmmfdr.

r-novice-inflammation

Software Carpentry introduction to R for novices using inflammation data.

r-pkgs

Building R packages

r-project-workflows

List of workflow tools for R projects

r-rastervis-feedstock

A conda-smithy repository for r-rastervis.

r-rcppgsl-feedstock

A conda-smithy repository for r-rcppgsl.

r-rmarkdown-feedstock

A conda-smithy repository for r-rmarkdown.

r-rsvg-feedstock

A conda-smithy repository for r-rsvg.

r-skimr-feedstock

A conda-smithy repository for r-skimr.

r-snpassoc-feedstock

A conda-smithy repository for r-snpassoc.

r-sparklyr-feedstock

A conda-smithy repository for r-sparklyr.

r-strucchange-feedstock

A conda-smithy repository for r-strucchange.

r-tidyselect-feedstock

A conda-smithy repository for r-tidyselect.

r-tidytext-feedstock

A conda-smithy repository for r-tidytext.

scde

R package for analyzing single-cell RNA-seq data

setup_vm

Installation scripts for virtual machine instances.

singlecell-qtl

null

singleCellSeq

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

Spoon-Knife

This repo is for demonstration purposes only.

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

swc-2015-04-17-nw

Software Carpentry Workshop at Northwestern University

swc-novice-r

Data files for teaching Software Carpentry novice R lessons

tbd

To be determined... -> TB Dissertation

tb-suscept

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

test-authorea

null

test-git

null

test-issue-templates

Temporary repo to test GitHub Issue Templates

test-push-pull

null

test-windows-push

null

tmpsite

Build R Markdown files in a temporary directory

umitools

Tools to handle reads sequenced with unique molecular identifiers (UMIs).

UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

UofCSCBC2012

A Software-Carpentry, Hacker Within Bootcamp at The University of Chicago, April 2-3, 2012.

wflow-build-undefined-variable

Reproducible example of unexpected wflow_build behavior

wflow-divvy

workflowr project for exploring the 2016 Divvy trip data.

workflowr

Organize your project into a research website

workflowrBeta

The beta release of workflowr

workflowr-demo01

An example site created with workflowr

workflowr-demo-archive

workflowr demo of archiving functionality

Commits To