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This project contains all scripts and descriptions to enable the execution of a streamlined pipeline that processes A-seq2 read libraries up to the reporting of individual and clustered 3' end processing sites.

Fork of the cathsm-server repo (https://github.com/CATH-SWISSMODEL/cathsm-server) for the tutorial "Beyond the usual Docker tutorial - Web apps & CI" at [BC]^2 Conference 2021

🐍 ☕ 🔩 🔧 A collection of commonly used Python helper functions.

☕ 🐍 🔬 Package for processing metadata from various light-microscopy related data formats.

xml input files for Beast, associated with manuscript: The Molecular Clock of Mycobacterium tuberculosis. DOI: https://doi.org/10.1371/journal.ppat.1008067

Analysis with exponential growth population prior, and 1/x prior on the clock rate

PowerShell based collector of Citrix metrics for Prometheus (creating a textfile for the windows_exporter).

User-friendly command-line interface for the ZARP RNA-Seq analysis pipeline

Metagenomics pipeline for human microbiome analysis with SnakeMake and singularity containers.

A public repository of the study "The sputum microbiome in pulmonary tuberculosis and its association with disease manifestations: a cross-sectional study within a prospective human cohort in Tanzania (TB-DAR)".

Associated publication: https://doi.org/10.3389/fmicb.2021.633396

Benchmark pipelines for the ProMod3 modelling engine

Peptide identification and quantification from MS data.

Very simple role to disable selinux and reboot the machine

scripts, pipelines and documentation to run PAQR and KAPAC

KAPAC allows to infer regulatory sequence motifs implicated in 3’ end processing changes

PAQR enables the quantification of poly(A) site usage from standard RNA-seq data

TACOS is a diverse Set Of Commands And Tools (SOCAT, but TACOS sounds much better!).