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    28 repositories

    • nf-quantseq

      Public
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Dec 12, 2024Dec 12, 2024

    • DRIMseq_script_Ultanir

      Public
      DRIMseq script used for APA analysis in Ultanir paper
      0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • rna_maps

      Public
      Plot CLIP crosslinks around regulated exons to study position-dependent impact on pre-mRNA splicing.
      Python
      •0•0•0•0•Updated Dec 10, 2024Dec 10, 2024

    • remove_spaces_in_fastq_headers

      Public
      remove spaces in fastq headers that can cause issues with STAR mapping followed by UMI duplicate removal
      Python
      •0•0•0•0•Updated Nov 29, 2024Nov 29, 2024

    • splicelogos

      Public
      generate human 5'ss and 3'ss logos
      R
      •0•0•0•0•Updated Sep 9, 2024Sep 9, 2024

    • nf-aws-test

      Public
      A short pipeline to test nf AWS batch performance
      Nextflow
      •0•0•0•0•Updated Jul 29, 2024Jul 29, 2024

    • peka

      Public
      Find motifs enriched around prominent crosslinks
      bioinformaticsbioinformatics-analysisbioinformatics-scripts
      Python
      •
      GNU General Public License v3.0
      •2•5•0•0•Updated Apr 29, 2024Apr 29, 2024

    • ultraplex

      Public
      Ultra-fast 5' and 3' demultiplexer
      Python
      •
      Other
      •12•26•20•0•Updated Apr 23, 2024Apr 23, 2024

    • LIN28A_RNPreassembly_bioinformatics

      Public
      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".
      Jupyter Notebook
      •0•1•0•0•Updated Mar 29, 2024Mar 29, 2024

    • clipplotr

      Public
      A tool to facilitate comparative visualisation of CLIP data
      data-visualisationcliprna-protein-interactions
      R
      •
      MIT License
      •5•14•1•0•Updated Nov 29, 2023Nov 29, 2023

    • cluster_kmers

      Public
      Get clusters of k-mers based solely on their sequence or in combination with enrichment in PEKA.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 21, 2023Nov 21, 2023

    • gtf-ops

      Public
      Filtering GENCODE or ENSEMBLE annotation in GTF format. Annotating missing regions in iCount genomic segmentation.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 29, 2023Sep 29, 2023

    • bs_assign

      Public
      Find groups of motifs around genomic landmarks of interest
      bioinformaticsbioinformatics-analysisbioinformatics-scripts
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 29, 2023Sep 29, 2023

    • cv_coverage

      Public
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Sep 28, 2023Sep 28, 2023

    • germ

      Public
      An algorithm for scoring Generalised RNA Multivalency
      R
      •
      MIT License
      •1•3•4•1•Updated Sep 14, 2023Sep 14, 2023

    • iCount-Mini

      Public
      iCount, protein-RNA interaction analytics
      Python
      •
      MIT License
      •26•1•2•0•Updated Jul 12, 2023Jul 12, 2023

    • ncawareclip

      Public
      iCLIP and miCLIP mapping pipeline to account for repetitive ncRNAs, especially snRNA, rRNA and tRNA.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 11, 2023Jan 11, 2023

    • clippy

      Public
      A wrapper around scipy "find_peaks" function to enable peak calling of CLIP data.
      Python
      •
      GNU General Public License v3.0
      •0•2•4•0•Updated Dec 1, 2022Dec 1, 2022

    • tdp43-mutants

      Public
      Repository for "TDP-43 condensation properties specify its RNA binding and regulatory repertoire"
      Jupyter Notebook
      •2•0•0•0•Updated Jun 22, 2022Jun 22, 2022

    • peka-eclip

      Public
      Download and prepare ENCODE eCLIP raw fastq for processing with the nf-core/clipseq pipeline
      clipnf-core
      Nextflow
      •
      GNU General Public License v3.0
      •3•1•0•0•Updated Jan 6, 2022Jan 6, 2022

    • clipseq

      Public
      CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
      Nextflow
      •
      MIT License
      •28•0•0•0•Updated Apr 27, 2021Apr 27, 2021

    • smallRNAs

      Public
      Sources of small RNAs used for pre-mapping.
      0•0•0•0•Updated Apr 19, 2021Apr 19, 2021

    • imaps

      Public
      Python
      •
      Apache License 2.0
      •3•0•0•0•Updated Nov 5, 2020Nov 5, 2020

    • non-coinciding_cDNA_starts

      Public
      R
      •0•4•0•0•Updated Jun 19, 2018Jun 19, 2018

    • clip-data-science

      Public
      Repository for Data Science Issues in Understanding Protein-RNA Interactions
      R
      •2•2•0•0•Updated Oct 24, 2017Oct 24, 2017

    • Alu-exonisation

      Public
      tools related to identification & characterisation of cryptic Alu-exons
      R
      •0•1•0•0•Updated Nov 2, 2016Nov 2, 2016

    • RBP-binding-sites

      Public
      Shell
      •1•0•1•0•Updated Jul 16, 2015Jul 16, 2015

    • STAU1_hiCLIP

      Public
      R
      •2•3•0•0•Updated Jan 7, 2015Jan 7, 2015