Pinned Repositories
clip-data-science
Repository for Data Science Issues in Understanding Protein-RNA Interactions
clipplotr
A tool to facilitate comparative visualisation of CLIP data
clippy
A wrapper around scipy "find_peaks" function to enable peak calling of CLIP data.
germ
An algorithm for scoring Generalised RNA Multivalency
iCount-Mini
iCount, protein-RNA interaction analytics
nf-quantseq
non-coinciding_cDNA_starts
peka
Find motifs enriched around prominent crosslinks
STAU1_hiCLIP
ultraplex
Ultra-fast 5' and 3' demultiplexer
ulelab's Repositories
ulelab/ultraplex
Ultra-fast 5' and 3' demultiplexer
ulelab/clipplotr
A tool to facilitate comparative visualisation of CLIP data
ulelab/peka
Find motifs enriched around prominent crosslinks
ulelab/non-coinciding_cDNA_starts
ulelab/germ
An algorithm for scoring Generalised RNA Multivalency
ulelab/STAU1_hiCLIP
ulelab/clip-data-science
Repository for Data Science Issues in Understanding Protein-RNA Interactions
ulelab/Alu-exonisation
tools related to identification & characterisation of cryptic Alu-exons
ulelab/clippy
A wrapper around scipy "find_peaks" function to enable peak calling of CLIP data.
ulelab/cv_coverage
ulelab/iCount-Mini
iCount, protein-RNA interaction analytics
ulelab/nf-quantseq
ulelab/peka-eclip
Download and prepare ENCODE eCLIP raw fastq for processing with the nf-core/clipseq pipeline
ulelab/bs_assign
Find groups of motifs around genomic landmarks of interest
ulelab/cluster_kmers
Get clusters of k-mers based solely on their sequence or in combination with enrichment in PEKA.
ulelab/gtf-ops
Filtering GENCODE or ENSEMBLE annotation in GTF format. Annotating missing regions in iCount genomic segmentation.
ulelab/imaps
ulelab/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".
ulelab/rna_maps
Plot CLIP crosslinks around regulated exons to study position-dependent impact on pre-mRNA splicing.
ulelab/tdp43-mutants
Repository for "TDP-43 condensation properties specify its RNA binding and regulatory repertoire"
ulelab/clipseq
CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
ulelab/ncawareclip
iCLIP and miCLIP mapping pipeline to account for repetitive ncRNAs, especially snRNA, rRNA and tRNA.
ulelab/nf-aws-test
A short pipeline to test nf AWS batch performance
ulelab/RBP-binding-sites
ulelab/smallRNAs
Sources of small RNAs used for pre-mapping.