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    34 repositories

    • flow.bio-paper-code

      Public
      Code for analyses presented in the Flow.bio paper
      HTML
      •0•0•0•0•Updated Jun 22, 2026Jun 22, 2026

    • flowAPIscripts

      Public
      build out scripts for upload, data download, trigger analysis
      Python
      •0•0•0•0•Updated Jun 19, 2026Jun 19, 2026

    • hnRNPH1_IR

      Public
      Exploring intron retention in HNRNPH1 and globally using multiple sequence alignment, intron retention scores, SpliceAI splice site strength inferences
      HTML
      •0•0•0•0•Updated Jun 11, 2026Jun 11, 2026

    • protocol-template

      Public template
      Reusable template for lab protocols.
      templatescientific-workflowslab-protocols
      templatescientific-workflowslab-protocols
      Python
      •
      MIT License
      •0•6•0•0•Updated Jun 9, 2026Jun 9, 2026

    • rna_maps

      Public
      Plot CLIP crosslinks around regulated exons to study position-dependent impact on pre-mRNA splicing.
      Python
      •3•0•0•0•Updated May 28, 2026May 28, 2026

    • RBPeek

      Public
      merge crosslinks files and intersect with BED for broad binding analysis and metaprofiling
      Python
      •0•0•0•0•Updated Apr 7, 2026Apr 7, 2026

    • iCount-Mini

      Public
      iCount, protein-RNA interaction analytics
      Python
      •
      MIT License
      •26•1•2•0•Updated Mar 2, 2026Mar 2, 2026

    • intron_retention_propensity

      Public
      Data, scripts, and figures pertaining to the exploration of intron retention across curated datasets for cell-type and developmental-stage specific interrogatio…
      HTML
      •0•0•0•0•Updated Jan 6, 2026Jan 6, 2026

    • PRMT-APA

      Public
      R
      •0•2•0•0•Updated Sep 22, 2025Sep 22, 2025

    • interstasis-paper

      Public
      A repository containing the code for Faraway et al. (2025).
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jul 21, 2025Jul 21, 2025

    • clippy

      Public
      A wrapper around scipy "find_peaks" function to enable peak calling of CLIP data.
      Python
      •
      GNU General Public License v3.0
      •0•3•6•0•Updated Jun 23, 2025Jun 23, 2025

    • nf-quantseq

      Public
      Nextflow
      •
      MIT License
      •1•1•0•0•Updated Jun 20, 2025Jun 20, 2025

    • 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 Mar 12, 2025Mar 12, 2025

    • 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
      bioinformaticsbioinformatics-analysisbioinformatics-scripts
      Python
      •
      GNU General Public License v3.0
      •2•7•2•0•Updated Apr 29, 2024Apr 29, 2024

    • ultraplex

      Public
      Ultra-fast 5' and 3' demultiplexer
      Python
      •
      Other
      •12•30•21•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-dep…
      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
      data-visualisationcliprna-protein-interactions
      R
      •
      MIT License
      •5•18•2•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

    • bs_assign

      Public
      Find groups of motifs around genomic landmarks of interest
      bioinformaticsbioinformatics-analysisbioinformatics-scripts
      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
      •2•6•4•1•Updated Sep 14, 2023Sep 14, 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

    • 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
      clipnf-core
      Nextflow
      •
      GNU General Public License v3.0
      •3•1•0•0•Updated Jan 6, 2022Jan 6, 2022

    • 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
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