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circular

R package for setting up and performing circRNA analysis from hcimeric read output, generated by the STAR aligner.

encircler

This package provides a user interface for uploading, reprocessing and performing circRNA quantification and identification from raw fastq files.

epigenbiotrain

Install scripts for all 30 Ubuntu computers

ghettoblast

This snakemake workflow imports a single fasta file with query sequences and blasts these against subject fasta files.

git

Git Source Code Mirror - This is a publish-only repository and all pull requests are ignored. Please follow Documentation/SubmittingPatches procedure for any of your improvements.

git4beginners

github4thewin

golem

A Framework for Building Robust Shiny Apps

junction_finder

liverdb

A snakemake workflow for automatically processing samples from NCBI GEO ID ids. This code is based on Tyler Weiricks pipeline for renaldb located here: https://bitbucket.org/tweirick/renaldb

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

pepper

Portable Encapsulated Project builder.

plasmidfindpipe

PlasmidFinder in a snakemake pipeline.

raw_reports

renaldb

A repository for a local setup of the RenalDB pipeline by Tyler Weirick at https://bitbucket.org/tweirick/renaldb

resfindersnake

ResFinder snakemake workflow

seq2science

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and RNA-seq workflows. Works equally easy with public as local data.

shinystar

A small Shiny package for interactively select fastq files for STAR alignment. The package uses system commands to initiate STAR aligner

shinystarindex

Mini app for STAR genome index generation

unix4beginners

Dataset for Unix introduction course

workflows-snakemake

One-day Snakemake workshop.

zzinflationr

A very small project (maybe future package) that aims to easily dispose of zero-inflation samples. Input data are gene (or Transcript) count tables, generated from RNA sequencing data.