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@YeoLab Yeo lab at UCSD

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    65 repositories

    • containers

      Public
      Collection of Dockerfiles
      Dockerfile
      •1•0•2•0•Updated Nov 8, 2024Nov 8, 2024

    • bento-tools

      Public
      A Python toolkit for subcellular analysis of spatial transcriptomics data
      Python
      •
      BSD 2-Clause "Simplified" License
      •6•70•17•1•Updated Nov 6, 2024Nov 6, 2024

    • HydRA

      Public
      Python
      •
      Other
      •2•9•0•0•Updated Oct 13, 2024Oct 13, 2024

    • PRINTER

      Public
      Codebase used to generate analysis for PRINTER manuscript.
      Jupyter Notebook
      •0•1•0•0•Updated Oct 1, 2024Oct 1, 2024

    • skipper

      Public
      Skip the peaks and expose RNA-binding in CLIP data
      R
      •
      Other
      •3•8•5•2•Updated Sep 27, 2024Sep 27, 2024

    • Mudskipper

      Public
      Python
      •0•0•0•0•Updated May 14, 2024May 14, 2024

    • FLARE

      Public
      RNA edit detection (SAILOR) and peak calling (FLARE)
      Python
      •
      Other
      •3•6•4•2•Updated Mar 27, 2024Mar 27, 2024

    • LR-Ribo-STAMP

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 21, 2024Feb 21, 2024

    • eclip-qc

      Public
      Python
      •0•0•5•0•Updated Jan 8, 2024Jan 8, 2024

    • CWL

      Public
      CWL Documents for commandlinetools and workflows
      0•0•0•0•Updated Sep 27, 2023Sep 27, 2023

    • qtools

      Public
      qtools has helper functions to submit jobs to compute clusters (PBS on TSCC, SGE on oolite) from within Python
      Python
      •
      Other
      •2•21•2•1•Updated Sep 20, 2023Sep 20, 2023

    • oligoCLIP

      Public
      pipeline for oligoCLIP
      Python
      •1•2•0•0•Updated Sep 8, 2023Sep 8, 2023

    • metadata-db

      Public
      Less
      •
      Other
      •0•0•4•1•Updated Aug 24, 2023Aug 24, 2023

    • maketrackhubs

      Public
      Python
      •0•0•1•0•Updated Jun 10, 2023Jun 10, 2023

    • clipper

      Public
      A tool to identify CLIP-seq peaks
      Python
      •
      Other
      •41•64•50•1•Updated Apr 27, 2023Apr 27, 2023

    • flotilla

      Public
      Reproducible machine learning analysis of gene expression and alternative splicing data
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •26•123•100•11•Updated Apr 15, 2023Apr 15, 2023

    • SONAR

      Public
      A program to construct SVM model and get classification scores for predicting RNA-binding proteins with given PPI network and RBP annotation list
      Python
      •
      Other
      •1•2•0•0•Updated Dec 27, 2022Dec 27, 2022

    • CRED-portal-v2

      Public
      CSS
      •0•0•0•0•Updated Dec 1, 2022Dec 1, 2022

    • eCLIP

      Public
      Common Workflow Language
      •
      Other
      •26•38•12•0•Updated Sep 29, 2022Sep 29, 2022

    • Metadensity

      Public
      Define metadensity to predict RNA binding protein function
      Shell
      •
      MIT License
      •2•0•0•0•Updated Aug 31, 2022Aug 31, 2022

    • yeolab.github.io

      Public
      Do not edit this repo! Everything here is machine-generated by Travis-CI every time we push to the yeolab/yeolab.github.io-source page
      HTML
      •3•1•0•1•Updated Aug 17, 2022Aug 17, 2022

    • yeolab.github.io-source

      Public archive
      🌊 Source code for http://yeolab.github.io/, autodeployed using Travis-CI
      Python
      •7•1•0•0•Updated Aug 17, 2022Aug 17, 2022

    • twenty-pelican-html5up

      Public
      This is an adaptation of the html5up template "Twenty" for the Python static site generator Pelican.
      HTML
      •
      Other
      •43•0•0•0•Updated Aug 17, 2022Aug 17, 2022

    • cshl_2022

      Public archive
      Collection of material to use for CSHL's Single Cell Analysis course 2022
      Jupyter Notebook
      •0•4•0•0•Updated Jul 13, 2022Jul 13, 2022

    • clip_analysis_legacy

      Public
      Python
      •1•1•1•0•Updated May 15, 2022May 15, 2022

    • rbp-maps

      Public
      splicing and feature maps for RBPs
      Python
      •10•24•4•0•Updated Apr 19, 2022Apr 19, 2022

    • merge_peaks

      Public
      Pipeline for using IDR to produce a set of peaks given two replicate eCLIP peaks
      Shell
      •7•9•10•1•Updated Feb 16, 2022Feb 16, 2022

    • chim-eCLIP

      Public
      chimeric eCLIP processing pipeline
      Common Workflow Language
      •
      MIT License
      •1•1•0•0•Updated Feb 4, 2022Feb 4, 2022

    • eclipdemux

      Public
      demultiplex utility for eclip raw fastq files (process eclip barcodes and ramdomers)
      Python
      •6•1•3•1•Updated Aug 27, 2021Aug 27, 2021

    • bam_to_bigwig

      Public
      A script to make stranded bigwig files from a bam file. Useful for STAMP edit C calculations.
      Shell
      •0•0•0•0•Updated Apr 26, 2021Apr 26, 2021