Zavolan Lab

All

40 repositories

zarp
Public
The Zavolab Automated RNA-seq Pipeline
docker workflow bioinformatics rna-seq snakemake pipeline reproducible-research conda singularity fair
Python
•
Apache License 2.0
•5•35•14•1•Updated Dec 19, 2024Dec 19, 2024
IPA-immune
Public
Python
•
Apache License 2.0
•0•0•1•0•Updated Dec 11, 2024Dec 11, 2024
htsinfer
Public
Infer metadata for your downstream analysis straight from your RNA-Seq data
bioinformatics ngs inference high-throughput-sequencing hacktoberfest
Python
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Apache License 2.0
•22•11•6•0•Updated Nov 20, 2024Nov 20, 2024
zarp-cli
Public
A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
python cli workflow library bioinformatics rna-seq snakemake pipeline reproducible-research sequencing
Python
•
Apache License 2.0
•1•5•9•0•Updated Nov 1, 2024Nov 1, 2024
SCINPAS
Public
Single Cell Identification of Novel PolyA Sites.
Python
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Apache License 2.0
•0•3•4•0•Updated Sep 18, 2024Sep 18, 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
mirflowz
Public
Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.
workflow bioinformatics snakemake mirna isomirs
Python
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MIT License
•1•6•26•2•Updated Aug 31, 2024Aug 31, 2024
experimental-determination-elongation-rates
Public
Python
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MIT License
•0•0•0•0•Updated Aug 22, 2024Aug 22, 2024
mapping-translation-rates
Public
Python
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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
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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
Python
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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 resulting data.
Nextflow
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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.
clip rna-binding-proteins bioinformatics
Python
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Apache License 2.0
•1•6•9•2•Updated Jan 24, 2023Jan 24, 2023
PAQR2
Public
Updated version of PAQR, which was previously available in the PAQR_KAPAC joint repository.
bioinformatics snakemake rna-seq-pipeline polyadenylation
Python
•
GNU General Public License v2.0
•0•7•4•1•Updated Dec 7, 2022Dec 7, 2022
Dockerfiles
Public
Dockerfile repository of the Zavolan Lab
Perl
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Apache License 2.0
•2•9•9•0•Updated Jul 8, 2022Jul 8, 2022
tandem-pas
Public
Extract set of tandem poly(A) sites from the PolyASite atlas.
bioinformatics snakemake polyadenylation
Perl
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Apache License 2.0
•0•2•2•0•Updated Feb 15, 2022Feb 15, 2022
bindz-rbp
Public
RBP module for bindz, a bioinformatics tool to detect regulators' binding sites on RNA sequences.
rna snakemake-workflows rna-binding-proteins bioinformatics-tool bioinformatics
Roff
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Apache License 2.0
•1•7•1•0•Updated Feb 14, 2022Feb 14, 2022
SCUREL
Public
Method to detect 3'UTR changes from scRNA-seq
scrnaseq snakemake-workflow bioinformatics
Python
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Apache License 2.0
•1•3•4•0•Updated Dec 16, 2021Dec 16, 2021
bindz-service
Public
Dockerfile
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Apache License 2.0
•0•1•0•0•Updated Nov 30, 2021Nov 30, 2021
PAQR_KAPAC
Public
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
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GNU General Public License v2.0
•4•8•9•0•Updated Nov 11, 2021Nov 11, 2021
tin-score-calculation
Public
Given a set of BAM files and a gene annotation BED file, calculates the Transcript Integrity Number (TIN) for each transcript.
bioinformatics quality-control rna-seq high-throughput-sequencing
Python
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GNU General Public License v3.0
•1•1•2•0•Updated Oct 29, 2021Oct 29, 2021
multiqc-plugins
Public
Custom plugins for the MultiQC tool.
bioinformatics high-throughput-sequencing bioinformatics-tool
HTML
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Apache License 2.0
•0•1•0•0•Updated Aug 24, 2021Aug 24, 2021
CFI2021
Public
Supplementary Materials
Jupyter Notebook
•0•0•0•0•Updated Jul 13, 2021Jul 13, 2021
zgtf
Public
gtf conversion utlity
genomics transcriptomics gtf-conversion-utlity
Python
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Apache License 2.0
•1•0•0•0•Updated Jun 17, 2021Jun 17, 2021
zpca
Public
PCA analysis
hacktoberfest
Python
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Apache License 2.0
•0•1•2•0•Updated Apr 9, 2021Apr 9, 2021
programming-for-life-sciences
Public archive
Toy repository for the Programming for Life Sciences course at the Biozentrum, University of Basel
teaching
Python
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Apache License 2.0
•3•4•0•0•Updated Oct 6, 2020Oct 6, 2020
merge_kallisto
Public
Merge kallisto results from multiple runs
R
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Apache License 2.0
•0•1•2•0•Updated Jun 18, 2020Jun 18, 2020
prune_tree
Public
Prune nh files based on a list of organisms
R
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Apache License 2.0
•0•0•0•0•Updated Jun 12, 2020Jun 12, 2020