zavolanlab repositories

55 repositories

APA_localization
Public
This repository is dedicated to lab's projects related to the studying of subcellular localization of alternative polyadenylation (APA) isoforms.
bioinformatics rna-seq collaboration
bioinformatics rna-seq collaboration alternative-polyadenylation
Python
•
MIT License
•0•0•0•0•Updated Sep 3, 2026Sep 3, 2026
pls-template
Public template
Python
•0•0•0•0•Updated Sep 1, 2026Sep 1, 2026
pls2026-course
Public
0•0•0•0•Updated Aug 27, 2026Aug 27, 2026
PAQR3
Public
PAQR3 is the updated version of the PAQR tool for quantifying poly(A) sites from bulk RNA-Seq data.
bioinformatics python3 alternative-polyadenylation
bioinformatics python3 alternative-polyadenylation
Python
•
MIT License
•0•0•1•0•Updated Aug 24, 2026Aug 24, 2026
crispr-projects
Public
This repository contains the computational workflows and downstream analysis notebooks related to CRISPR projects in Zavolan lab.
bioinformatics snakemake analysis
bioinformatics snakemake analysis crispr
Python
•
MIT License
•0•0•0•0•Updated Aug 14, 2026Aug 14, 2026
zavolab_pyutils
Public
This repository contains python modules dedicated to various utilities for genomic data analysis, like library size normalization, annotation conversion etc
bioinformatics python3
bioinformatics python3
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Aug 11, 2026Aug 11, 2026
nanoflowz
Public
This repository contains a set of workflows and tools for processing and analysis of ONT RNA long-read sequencing data
workflow bioinformatics nextflow
workflow bioinformatics nextflow nanopore-sequencing
Python
•
MIT License
•0•1•3•1•Updated Aug 6, 2026Aug 6, 2026
mirflowz
Public
Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.
workflow bioinformatics snakemake
workflow bioinformatics snakemake mirna isomirs
Python
•
MIT License
•1•6•18•1•Updated Jul 16, 2026Jul 16, 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…
bioinformatics nanopore-sequencing hondele
bioinformatics nanopore-sequencing hondele
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Jun 17, 2026Jun 17, 2026
SCINPAS
Public
Single Cell Identification of Novel PolyA Sites.
bioinformatics nextflow alternative-polyadenylation
bioinformatics nextflow alternative-polyadenylation
Python
•
Apache License 2.0
•0•4•4•0•Updated May 12, 2026May 12, 2026
IPA-immune
Public
Python
•
Apache License 2.0
•0•0•1•0•Updated May 11, 2026May 11, 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
bioinformatics alternative-polyadenylation
bioinformatics alternative-polyadenylation
Jupyter Notebook
•
MIT License
•0•1•0•0•Updated May 8, 2026May 8, 2026
pbody_RNA_Spang
Public
This repository stores computational workflows and downstream analysis notebooks related to the analysis of P-body associated RNA, based on RNA-seq and cCLAP ex…
bioinformatics rna-seq collaboration
bioinformatics rna-seq collaboration spang cclap
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Apr 22, 2026Apr 22, 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…
bioinformatics rna-seq collaboration
bioinformatics rna-seq collaboration spang
Python
•
MIT License
•0•0•0•0•Updated Apr 15, 2026Apr 15, 2026
SeqMetrics
Public
Package to compute metrics over protein-coding sequences
Python
•
MIT License
•0•0•0•0•Updated Apr 10, 2026Apr 10, 2026
ucsc_tracks
Public
This repository is dedicated to store the tracks for visualization in UCSC Genome Browser, from various studies
MIT License
•0•0•0•0•Updated Feb 10, 2026Feb 10, 2026
zarp
Public
The Zavolab Automated RNA-seq Pipeline
docker workflow bioinformatics
docker workflow bioinformatics rna-seq snakemake pipeline reproducible-research conda singularity fair
Python
•
Apache License 2.0
•4•36•12•0•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
•0•0•0•0•Updated Aug 29, 2025Aug 29, 2025
zarp-cli
Public
A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
python cli workflow
python cli workflow library bioinformatics rna-seq snakemake pipeline reproducible-research sequencing
Python
•
Apache License 2.0
•2•6•9•1•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
0•0•0•0•Updated May 9, 2025May 9, 2025
htsinfer
Public
Infer metadata for your downstream analysis straight from your RNA-Seq data
bioinformatics ngs inference
bioinformatics ngs inference high-throughput-sequencing hacktoberfest
Python
•
Apache License 2.0
•21•15•6•0•Updated Nov 20, 2024Nov 20, 2024
polyAsite_Atlas_3
Public
The repository contains the data related to polyAsite Atlas v3 database and paper
HTML
•0•0•0•0•Updated Sep 11, 2024Sep 11, 2024
experimental-determination-elongation-rates
Public
Python
•
MIT License
•0•0•0•0•Updated Aug 22, 2024Aug 22, 2024
mapping-translation-rates
Public
Python
•
MIT License
•0•0•0•0•Updated Aug 22, 2024Aug 22, 2024
bCLIP_Stefanie_Jonas
Public
Jupyter Notebook
•0•0•0•0•Updated Jul 2, 2024Jul 2, 2024
logo
Public
Zavolab logo
Creative Commons Zero v1.0 Universal
•0•0•0•0•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
•0•0•0•0•Updated Nov 13, 2023Nov 13, 2023
scRNAsim-toolz
Public
A repository for the tools used by scRNAsim.
bioinformatics simulation scrna-seq
bioinformatics simulation scrna-seq
Python
•
MIT License
•0•1•11•0•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
•0•0•5•0•Updated Oct 23, 2023Oct 23, 2023
RCRUNCH
Public
Workflow for automated (e)CLIP analysis. From raw fastq to peak calling and motif analysis.
bioinformatics clip rna-binding-proteins
bioinformatics clip rna-binding-proteins
Python
•
Apache License 2.0
•1•6•11•2•Updated Jan 24, 2023Jan 24, 2023

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Zavolan Lab

All

55 repositories

APA_localization

pls-template

pls2026-course

PAQR3

crispr-projects

zavolab_pyutils

nanoflowz

mirflowz

ONT_seq_PAIP1_Hondele

SCINPAS

IPA-immune

CellType_PolyASite_Atlas

pbody_RNA_Spang

TemperatureDependentCelegansAging_Spang

SeqMetrics

ucsc_tracks

zarp

primer_probe_design

zarp-cli

rcrunch_ENCODE_RBPs_trackhub

htsinfer

polyAsite_Atlas_3

experimental-determination-elongation-rates

mapping-translation-rates

bCLIP_Stefanie_Jonas

logo

oligomap

scRNAsim-toolz

scRNAsim

RCRUNCH

Repositories list

55 repositories