Zavolan Lab

zarp

The Zavolab Automated RNA-seq Pipeline

htsinfer

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

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.

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.

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.

scRNAsim-toolz

A repository for the tools used by scRNAsim.

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

zgtf

gtf conversion utlity

bCLIP_Stefanie_Jonas

IPA-immune

logo

Zavolab logo

oligomap

Oligomap is a program for fast identification of nearly-perfect matches of small RNAs in sequence databases.

polyAsite_Atlas_3

The repository contains the data related to polyAsite Atlas v3 database and paper

prune_tree

Prune nh files based on a list of organisms

scRNAsim

The projects implements a simulation of single cell RNA sequencing (scRNA-seq), accounting for some common sources noise that complicate the analysis of the resulting data.