Zavolan Lab (@zavolanlab)
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Top repositories

1

zarp

The Zavolab Automated RNA-seq Pipeline
Python
34
star
2

htsinfer

Infer metadata for your downstream analysis straight from your RNA-seq data
Python
10
star
3

polyAsite_workflow

Pipeline for the processing of 3' end sequencing libraries
Python
9
star
4

Dockerfiles

Dockerfile repository of the Zavolan Lab
Perl
9
star
5

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
Python
8
star
6

PAQR2

Updated version of PAQR, which was previously available in the PAQR_KAPAC joint repository.
Python
7
star
7

TECtool

TECtool uses mRNA and 3’ end sequencing data to identify novel terminal exons.
Python
7
star
8

RCRUNCH

Workflow for automated (e)CLIP analysis. From raw fastq to peak calling and motif analysis.
Python
6
star
9

bindz-rbp

RBP module for bindz, a bioinformatics tool to detect regulators' binding sites on RNA sequences.
Roff
6
star
10

MIRZAG

MIRZA-G - Pipeline and model for miRNA target prediction
Python
5
star
11

zarp-cli

A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
Python
5
star
12

programming-for-life-sciences

Toy repository for the Programming for Life Sciences course at the Biozentrum, University of Basel
Python
4
star
13

mirflowz

Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.
Python
3
star
14

SCUREL

Method to detect 3'UTR changes from scRNA-seq
Python
3
star
15

snoRNAHybridSearchPipeline

A pipeline to discover snoRNA-target chimeric reads in CLIP/HTS experiments.
Python
2
star
16

SCINPAS

Single Cell Identification of Novel PolyA Sites.
Python
2
star
17

CWL_repository

Zavolan-Lab repository for CWL Tools and Workflows
Common Workflow Language
2
star
18

tandem-pas

Extract set of tandem poly(A) sites from the PolyASite atlas.
Perl
2
star
19

srsf1_selex_Allain_lab

Notebook of SELEX data analysis
Jupyter Notebook
2
star
20

scRNAsim-toolz

A repository for the tools used by scRNAsim.
Python
1
star
21

multiqc-plugins

Custom plugins for the MultiQC tool.
HTML
1
star
22

zpca

PCA analysis
Python
1
star
23

bindz-service

Dockerfile
1
star
24

tin-score-calculation

Given a set of BAM files and a gene annotation BED file, calculates the Transcript Integrity Number (TIN) for each transcript.
Python
1
star