Ulelab

ultraplex

Ultra-fast 5' and 3' demultiplexer

clipplotr

A tool to facilitate comparative visualisation of CLIP data

peka

Find motifs enriched around prominent crosslinks

non-coinciding_cDNA_starts

germ

An algorithm for scoring Generalised RNA Multivalency

STAU1_hiCLIP

clip-data-science

Repository for Data Science Issues in Understanding Protein-RNA Interactions

Alu-exonisation

tools related to identification & characterisation of cryptic Alu-exons

clippy

A wrapper around scipy "find_peaks" function to enable peak calling of CLIP data.

cv_coverage

iCount-Mini

iCount, protein-RNA interaction analytics

nf-quantseq

peka-eclip

Download and prepare ENCODE eCLIP raw fastq for processing with the nf-core/clipseq pipeline

bs_assign

Find groups of motifs around genomic landmarks of interest

cluster_kmers

Get clusters of k-mers based solely on their sequence or in combination with enrichment in PEKA.

gtf-ops

Filtering GENCODE or ENSEMBLE annotation in GTF format. Annotating missing regions in iCount genomic segmentation.

imaps

LIN28A_RNPreassembly_bioinformatics

This repository contains the source code used for bioinformatic analyses presented in the paper by Modic et al., 2024 "Poised PABP-RNA hubs implement signal-dependent mRNA decay in development".

tdp43-mutants

Repository for "TDP-43 condensation properties specify its RNA binding and regulatory repertoire"

clipseq

CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

ncawareclip

iCLIP and miCLIP mapping pipeline to account for repetitive ncRNAs, especially snRNA, rRNA and tRNA.

RBP-binding-sites

rna_maps

Plot CLIP crosslinks around regulated exons to study position-dependent impact on pre-mRNA splicing.

smallRNAs

Sources of small RNAs used for pre-mapping.