Pinned Repositories
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
KasperThystrup's Repositories
KasperThystrup/circulaR
R package for setting up and performing circRNA analysis from hcimeric read output, generated by the STAR aligner.
KasperThystrup/EncircleR
This package provides a user interface for uploading, reprocessing and performing circRNA quantification and identification from raw fastq files.
KasperThystrup/EpiGenBioTrain
Install scripts for all 30 Ubuntu computers
KasperThystrup/ghettoblast
This snakemake workflow imports a single fasta file with query sequences and blasts these against subject fasta files.
KasperThystrup/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.
KasperThystrup/git4beginners
KasperThystrup/github4thewin
KasperThystrup/golem
A Framework for Building Robust Shiny Apps
KasperThystrup/junction_finder
KasperThystrup/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
KasperThystrup/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
KasperThystrup/PEPper
Portable Encapsulated Project builder.
KasperThystrup/PlasmidFindPipe
PlasmidFinder in a snakemake pipeline.
KasperThystrup/raw_reports
KasperThystrup/renaldb
A repository for a local setup of the RenalDB pipeline by Tyler Weirick at https://bitbucket.org/tweirick/renaldb
KasperThystrup/ResFinderSnake
ResFinder snakemake workflow
KasperThystrup/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.
KasperThystrup/ShinySTAR
A small Shiny package for interactively select fastq files for STAR alignment. The package uses system commands to initiate STAR aligner
KasperThystrup/ShinyStarIndex
Mini app for STAR genome index generation
KasperThystrup/Unix4Beginners
Dataset for Unix introduction course
KasperThystrup/workflows-snakemake
One-day Snakemake workshop.
KasperThystrup/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.