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bcl2fastq

bcl2fastq by Illumina

cage-dzne

CAGE-related toolset

centrifuge-1.0.4-beta

Centrifuge 1.0.4-beta from 10. June 2018. Includes script for bacterial, viral and archaea DB

kraken-bracken

kraken2-bracken

Updated KRAKEN2+BRACKEN Docker image with the newest version of Kraken (to escape rsync problem when downloading the libraries)

kraken2.0.7-beta

Kraken2.0.7-beta edited

lncid_to_ensg

Dictionary for translating LNC and other trivial gene IDs to Ensembl ENSG ID (H.sapiens)

machine-learning-in-single-cell-biology

A collection of scripts created as solutions for assignments in the course Machine Learning for Single Cell Biology.

mapping_viz_collection

Collection of useful tools for paper-grade mapping viz (and all intermediate steps necessary)

oh-know

repository for the oh-know workshop

pbc_plot

Per base coverage statistics pipeline to assess the expected versus factual coverage of the reference sequence region by the newly sequenced reads (arrival-like statistics). Plots the per base coverage, helping visualize the possible sequencing\mapping pitfalls and repetative region collapses.

repeatmodeler_docker

RepeatModeler Docker

simulation_manuscript

Generalized scripts used for simulation and subsequent benchmarking of the various TE expression tools.

squire-for-docker

starmap

Simple nextflow pipeline to map reads and, if needed, generate genome index

telocal_gentable

R script to merge all count tables output by TElocal into one for multiple samples. It also separates the gene counts into a separate table. Additionally, it aggregates the counts for subfamilies of transposons.

trimnsquire

Trim your fastqs and SQuIRE them up!