Zavolan Lab's repositories

zarp

The Zavolab Automated RNA-seq Pipeline

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htsinfer

Infer metadata for your downstream analysis straight from your RNA-seq data

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polyAsite_workflow

Pipeline for the processing of 3' end sequencing libraries

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Dockerfiles

Dockerfile repository of the Zavolan Lab

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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

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PAQR2

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

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bindz-rbp

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

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RCRUNCH

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

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mirflowz

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

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programming-for-life-sciences

Toy repository for the Programming for Life Sciences course at the Biozentrum, University of Basel

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zarp-cli

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

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SCUREL

Method to detect 3'UTR changes from scRNA-seq

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CWL_repository

Zavolan-Lab repository for CWL Tools and Workflows

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SCINPAS

Single Cell Identification of Novel PolyA Sites.

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srsf1_selex_Allain_lab

Notebook of SELEX data analysis

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tandem-pas

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

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merge_kallisto

Merge kallisto results from multiple runs

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multiqc-plugins

Custom plugins for the MultiQC tool.

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scRNAsim-toolz

A repository for the tools used by scRNAsim.

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tin-score-calculation

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

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zpca

PCA analysis

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CFI2021

Supplementary Materials

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zgtf

gtf conversion utlity

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logo

Zavolab logo

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oligomap

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

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polyAsite_Atlas_3

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

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prune_tree

Prune nh files based on a list of organisms

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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.

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