zavolanlab/RCRUNCH

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Language
Python
License
Apache License 2.0
Created over 2 years ago
Updated almost 2 years ago

zavolanlab/RCRUNCH

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

zarp

The Zavolab Automated RNA-seq Pipeline

htsinfer

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

polyAsite_workflow

Pipeline for the processing of 3' end sequencing libraries

Dockerfiles

Dockerfile repository of the Zavolan Lab

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

PAQR2

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

TECtool

TECtool uses mRNA and 3’ end sequencing data to identify novel terminal exons.

bindz-rbp

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

MIRZAG

MIRZA-G - Pipeline and model for miRNA target prediction

zarp-cli

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

programming-for-life-sciences

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

mirflowz

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

SCUREL

Method to detect 3'UTR changes from scRNA-seq

snoRNAHybridSearchPipeline

A pipeline to discover snoRNA-target chimeric reads in CLIP/HTS experiments.

SCINPAS

Single Cell Identification of Novel PolyA Sites.

CWL_repository

Zavolan-Lab repository for CWL Tools and Workflows

Common Workflow Language

tandem-pas

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

srsf1_selex_Allain_lab

Notebook of SELEX data analysis

Jupyter Notebook

scRNAsim-toolz

A repository for the tools used by scRNAsim.

multiqc-plugins

Custom plugins for the MultiQC tool.

zpca

bindz-service

tin-score-calculation

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