Repositories list

• nanoflowz

  Public
  This repository contains a set of workflows and tools for processing and analysis of ONT RNA long-read sequencing data

  workflowbioinformaticsnextflow+ 1

  workflowbioinformaticsnextflownanopore-sequencing

  Python

  •

  MIT License

  •00 forks•11 star•66 issues•11 pull request•Updated Apr 24, 2026Apr 24, 2026

• CellType_PolyASite_Atlas

  Public
  This repository is dedicated to the update of PolyASite Atlas to v4.0 with cell-type-level quantification of PAS usage

  bioinformaticsalternative-polyadenylation

  bioinformaticsalternative-polyadenylation

  Jupyter Notebook

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• SCINPAS

  Public
  Single Cell Identification of Novel PolyA Sites.

  bioinformaticsnextflowalternative-polyadenylation

  bioinformaticsnextflowalternative-polyadenylation

  Python

  •

  Apache License 2.0

  •00 forks•44 stars•44 issues•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• ONT_seq_PAIP1_Hondele

  Public
  This repository contains the computational workflows and downstream analysis notebooks related to the polyA tail length changes linked to PAIP1 perturbations, c…

  bioinformaticsnanopore-sequencinghondele

  bioinformaticsnanopore-sequencinghondele

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• zavolab_pyutils

  Public
  This repository contains python modules dedicated to various utilities for genomic data analysis, like library size normalization, annotation conversion etc

  bioinformaticspython3

  bioinformaticspython3

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• APA_localization

  Public
  This repository is dedicated to lab's projects related to the studying of subcellular localization of alternative polyadenylation (APA) isoforms.

  bioinformaticsrna-seqcollaboration+ 1

  bioinformaticsrna-seqcollaborationalternative-polyadenylation

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• TemperatureDependentCelegansAging_Spang

  Public
  This repository contains the computational workflows and downstream analysis notebooks related to the experiments on Temperature-Dependent C.elegans Aging condu…

  bioinformaticsrna-seqcollaboration+ 1

  bioinformaticsrna-seqcollaborationspang

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• SeqMetrics

  Public
  Package to compute metrics over protein-coding sequences

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• mirflowz

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

  workflowbioinformaticssnakemake+ 2

  workflowbioinformaticssnakemakemirnaisomirs

  Python

  •

  MIT License

  •11 fork•66 stars•1919 issues•11 pull request•Updated Apr 4, 2026Apr 4, 2026

• ucsc_tracks

  Public
  This repository is dedicated to store the tracks for visualization in UCSC Genome Browser, from various studies

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 10, 2026Feb 10, 2026

• zarp

  Public
  The Zavolab Automated RNA-seq Pipeline

  dockerworkflowbioinformatics+ 9

  dockerworkflowbioinformaticsrna-seqsnakemakepipelinereproducible-researchcondasingularityfair+ 2

  Python

  •

  Apache License 2.0

  •44 forks•3636 stars•1212 issues•00 pull requests•Updated Jan 29, 2026Jan 29, 2026

• primer_probe_design

  Public
  The repository contains the data, UCSC trackhub, and tools for PCR primer and probe design in the Zavolan lab

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 29, 2025Aug 29, 2025

• zarp-cli

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

  pythoncliworkflow+ 11

  pythoncliworkflowlibrarybioinformaticsrna-seqsnakemakepipelinereproducible-researchsequencing+ 4

  Python

  •

  Apache License 2.0

  •11 fork•66 stars•99 issues•11 pull request•Updated Aug 26, 2025Aug 26, 2025

• rcrunch_ENCODE_RBPs_trackhub

  Public
  This repository contains the files for the TrackHub based on the RCRUNCH processing of ENCODE RBP eCLIP data

  00 forks•00 stars•00 issues•00 pull requests•Updated May 9, 2025May 9, 2025

• IPA-immune

  Public
  Python

  •

  Apache License 2.0

  •00 forks•00 stars•11 issue•00 pull requests•Updated Jan 7, 2025Jan 7, 2025

• htsinfer

  Public
  Infer metadata for your downstream analysis straight from your RNA-Seq data

  bioinformaticsngsinference+ 2

  bioinformaticsngsinferencehigh-throughput-sequencinghacktoberfest

  Python

  •

  Apache License 2.0

  •2222 forks•1515 stars•66 issues•00 pull requests•Updated Nov 20, 2024Nov 20, 2024

• polyAsite_Atlas_3

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

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 11, 2024Sep 11, 2024

• experimental-determination-elongation-rates

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 22, 2024Aug 22, 2024

• mapping-translation-rates

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 22, 2024Aug 22, 2024

• bCLIP_Stefanie_Jonas

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 2, 2024Jul 2, 2024

• logo

  Public
  Zavolab logo

  Creative Commons Zero v1.0 Universal

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 3, 2024Feb 3, 2024

• oligomap

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

  Shell

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 13, 2023Nov 13, 2023

• scRNAsim-toolz

  Public
  A repository for the tools used by scRNAsim.

  bioinformaticssimulationscrna-seq

  bioinformaticssimulationscrna-seq

  Python

  •

  MIT License

  •00 forks•11 star•1111 issues•00 pull requests•Updated Oct 27, 2023Oct 27, 2023

• scRNAsim

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

  Nextflow

  •

  MIT License

  •00 forks•00 stars•55 issues•00 pull requests•Updated Oct 23, 2023Oct 23, 2023

• RCRUNCH

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

  bioinformaticscliprna-binding-proteins

  bioinformaticscliprna-binding-proteins

  Python

  •

  Apache License 2.0

  •11 fork•66 stars•1111 issues•22 pull requests•Updated Jan 24, 2023Jan 24, 2023

• PAQR2

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

  bioinformaticssnakemakerna-seq-pipeline+ 1

  bioinformaticssnakemakerna-seq-pipelinepolyadenylation

  Python

  •

  GNU General Public License v2.0

  •00 forks•66 stars•55 issues•11 pull request•Updated Dec 7, 2022Dec 7, 2022

• Dockerfiles

  Public
  Dockerfile repository of the Zavolan Lab

  Perl

  •

  Apache License 2.0

  •22 forks•88 stars•99 issues•00 pull requests•Updated Jul 8, 2022Jul 8, 2022

• tandem-pas

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

  bioinformaticssnakemakepolyadenylation

  bioinformaticssnakemakepolyadenylation

  Perl

  •

  Apache License 2.0

  •00 forks•11 star•22 issues•00 pull requests•Updated Feb 15, 2022Feb 15, 2022

• bindz-rbp

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

  bioinformaticsrnasnakemake-workflows+ 2

  bioinformaticsrnasnakemake-workflowsrna-binding-proteinsbioinformatics-tool

  Roff

  •

  Apache License 2.0

  •00 forks•88 stars•11 issue•00 pull requests•Updated Feb 14, 2022Feb 14, 2022

• SCUREL

  Public
  Method to detect 3'UTR changes from scRNA-seq

  bioinformaticsscrnaseqsnakemake-workflow

  bioinformaticsscrnaseqsnakemake-workflow

  Python

  •

  Apache License 2.0

  •11 fork•22 stars•44 issues•00 pull requests•Updated Dec 16, 2021Dec 16, 2021