Pinned Repositories
bindz-rbp
RBP module for bindz, a bioinformatics tool to detect regulators' binding sites on RNA sequences.
Dockerfiles
Dockerfile repository of the Zavolan Lab
htsinfer
Infer metadata for your downstream analysis straight from your RNA-seq data
mirflowz
Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.
PAQR2
Updated version of PAQR, which was previously available in the PAQR_KAPAC joint repository.
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
polyAsite_workflow
Pipeline for the processing of 3' end sequencing libraries
RCRUNCH
Workflow for automated (e)CLIP analysis. From raw fastq to peak calling and motif analysis.
TECtool
TECtool uses mRNA and 3’ end sequencing data to identify novel terminal exons.
zarp
The Zavolab Automated RNA-seq Pipeline
Zavolan Lab's Repositories
zavolanlab/zarp
The Zavolab Automated RNA-seq Pipeline
zavolanlab/htsinfer
Infer metadata for your downstream analysis straight from your RNA-seq data
zavolanlab/Dockerfiles
Dockerfile repository of the Zavolan Lab
zavolanlab/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
zavolanlab/PAQR2
Updated version of PAQR, which was previously available in the PAQR_KAPAC joint repository.
zavolanlab/bindz-rbp
RBP module for bindz, a bioinformatics tool to detect regulators' binding sites on RNA sequences.
zavolanlab/mirflowz
Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.
zavolanlab/RCRUNCH
Workflow for automated (e)CLIP analysis. From raw fastq to peak calling and motif analysis.
zavolanlab/zarp-cli
A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
zavolanlab/programming-for-life-sciences
Toy repository for the Programming for Life Sciences course at the Biozentrum, University of Basel
zavolanlab/SCUREL
Method to detect 3'UTR changes from scRNA-seq
zavolanlab/SCINPAS
Single Cell Identification of Novel PolyA Sites.
zavolanlab/tandem-pas
Extract set of tandem poly(A) sites from the PolyASite atlas.
zavolanlab/bindz-service
zavolanlab/merge_kallisto
Merge kallisto results from multiple runs
zavolanlab/multiqc-plugins
Custom plugins for the MultiQC tool.
zavolanlab/scRNAsim-toolz
A repository for the tools used by scRNAsim.
zavolanlab/tin-score-calculation
Given a set of BAM files and a gene annotation BED file, calculates the Transcript Integrity Number (TIN) for each transcript.
zavolanlab/zpca
PCA analysis
zavolanlab/CFI2021
Supplementary Materials
zavolanlab/IPA-immune
zavolanlab/oligomap
Oligomap is a program for fast identification of nearly-perfect matches of small RNAs in sequence databases.
zavolanlab/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.
zavolanlab/zgtf
gtf conversion utlity
zavolanlab/bCLIP_Stefanie_Jonas
zavolanlab/experimental-determination-elongation-rates
zavolanlab/logo
Zavolab logo
zavolanlab/mapping-translation-rates
zavolanlab/polyAsite_Atlas_3
The repository contains the data related to polyAsite Atlas v3 database and paper
zavolanlab/prune_tree
Prune nh files based on a list of organisms