Zavolan Lab

zarp

The Zavolab Automated RNA-seq Pipeline

htsinfer

Infer metadata for your downstream analysis straight from your RNA-seq data

polyAsite_workflow

Pipeline for the processing of 3' end sequencing libraries

Dockerfiles

Dockerfile repository of the Zavolan Lab

PAQR_KAPAC

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

PAQR2

Updated version of PAQR, which was previously available in the PAQR_KAPAC joint repository.

TECtool

TECtool uses mRNA and 3’ end sequencing data to identify novel terminal exons.

bindz-rbp

RBP module for bindz, a bioinformatics tool to detect regulators' binding sites on RNA sequences.

mirflowz

Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.

RCRUNCH

Workflow for automated (e)CLIP analysis. From raw fastq to peak calling and motif analysis.

MIRZAG

MIRZA-G - Pipeline and model for miRNA target prediction

programming-for-life-sciences

Toy repository for the Programming for Life Sciences course at the Biozentrum, University of Basel

zarp-cli

A user-friendly command-line interface for the ZARP RNA-seq analysis workflow

SCUREL

Method to detect 3'UTR changes from scRNA-seq

CWL_repository

Zavolan-Lab repository for CWL Tools and Workflows

SCINPAS

Single Cell Identification of Novel PolyA Sites.

srsf1_selex_Allain_lab

Notebook of SELEX data analysis

tandem-pas

Extract set of tandem poly(A) sites from the PolyASite atlas.

bindz-service

merge_kallisto

Merge kallisto results from multiple runs

multiqc-plugins

Custom plugins for the MultiQC tool.

tin-score-calculation

Given a set of BAM files and a gene annotation BED file, calculates the Transcript Integrity Number (TIN) for each transcript.

zpca

PCA analysis

CFI2021

Supplementary Materials

Liver3DCulture

zgtf

gtf conversion utlity

IsoformQuantificationBenchmarking

Comparative assessment of methods for the computational inference of transcript isoform from RNA-seq data. Submitted to Genome Biology (03-2015).

logo

Zavolab logo

prune_tree

Prune nh files based on a list of organisms

snakemake_example_workflow

Snakemake example workflow with singularity