ulelab/peka

Find motifs enriched around prominent crosslinks

Language: Python - Size: 31.9 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 4 - Forks: 2

ulelab/ultraplex

Ultra-fast 5' and 3' demultiplexer

Language: Python - Size: 5.09 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 21 - Forks: 8

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".

Language: Jupyter Notebook - Size: 36 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

ulelab/clipplotr

A tool to facilitate comparative visualisation of CLIP data

Language: R - Size: 55.9 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 11 - Forks: 4

ulelab/cluster_kmers

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

Language: Python - Size: 1.29 MB - Last synced: 6 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

ulelab/STAU1_hiCLIP

Language: R - Size: 258 KB - Last synced: 8 months ago - Pushed: over 9 years ago - Stars: 3 - Forks: 2

ulelab/gtf-ops

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

Language: Python - Size: 49.2 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

ulelab/bs_assign

Find groups of motifs around genomic landmarks of interest

Language: Python - Size: 34.2 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

ulelab/germ

An algorithm for scoring Generalised RNA Multivalency

Language: R - Size: 2.82 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 1 - Forks: 0

ulelab/clippy

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

Language: Python - Size: 88.9 MB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

ulelab/iCount-Mini Fork of genialis/iCount

iCount, protein-RNA interaction analytics

Language: Python - Size: 26 MB - Last synced: 3 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 0

ulelab/nf-quantseq

Language: Nextflow - Size: 24.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

ulelab/peka-eclip

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

Language: Nextflow - Size: 37.1 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 1

ulelab/ncawareclip

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

Language: Python - Size: 104 KB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

ulelab/cv_coverage

Language: Python - Size: 84 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

ulelab/tdp43-mutants

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

Language: Jupyter Notebook - Size: 3.89 MB - Last synced: over 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1

ulelab/clipseq Fork of nf-core/clipseq

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

Size: 39.2 MB - Last synced: over 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

ulelab/smallRNAs

Sources of small RNAs used for pre-mapping.

Size: 2.93 KB - Last synced: over 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

ulelab/non-coinciding_cDNA_starts

Language: R - Size: 23.6 MB - Last synced: over 1 year ago - Pushed: almost 6 years ago - Stars: 4 - Forks: 0

ulelab/imaps

Language: Python - Size: 128 KB - Last synced: 29 days ago - Pushed: over 3 years ago - Stars: 0 - Forks: 4

ulelab/RBP-binding-sites

Language: Shell - Size: 146 KB - Last synced: over 1 year ago - Pushed: almost 9 years ago - Stars: 0 - Forks: 1

ulelab/Alu-exonisation

tools related to identification & characterisation of cryptic Alu-exons

Language: R - Size: 6.48 MB - Last synced: over 1 year ago - Pushed: over 7 years ago - Stars: 1 - Forks: 0

ulelab/clip-data-science

Repository for Data Science Issues in Understanding Protein-RNA Interactions

Language: R - Size: 13.7 KB - Last synced: over 1 year ago - Pushed: over 6 years ago - Stars: 2 - Forks: 2