Yeo lab at UCSD

flotilla

Reproducible machine learning analysis of gene expression and alternative splicing data

clipper

A tool to identify CLIP-seq peaks

eCLIP

rbp-maps

splicing and feature maps for RBPs

qtools

qtools has helper functions to submit jobs to compute clusters (PBS on TSCC, SGE on oolite) from within Python

HydRA

merge_peaks

Pipeline for using IDR to produce a set of peaks given two replicate eCLIP peaks

skipper

Skip the peaks and expose RNA-binding in CLIP data

repetitive-element-mapping

pipeline for mapping repetitive elements

cshl_2022

Collection of material to use for CSHL's Single Cell Analysis course 2022

FLARE

RNA edit detection (SAILOR) and peak calling (FLARE)

Yeo_STAMP_Nature_Methods

Code repository for "Robust single-cell discovery of RNA targets of RNA binding proteins and ribosome"

oligoCLIP

pipeline for oligoCLIP

SONAR

A program to construct SVM model and get classification scores for predicting RNA-binding proteins with given PPI network and RBP annotation list

chim-eCLIP

chimeric eCLIP processing pipeline

clip_analysis_legacy

eclipdemux

demultiplex utility for eclip raw fastq files (process eclip barcodes and ramdomers)

PRINTER

Codebase used to generate analysis for PRINTER manuscript.

yeolab.github.io

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

yeolab.github.io-source

:ocean: Source code for http://yeolab.github.io/, autodeployed using Travis-CI

bam_to_bigwig

A script to make stranded bigwig files from a bam file. Useful for STAMP edit C calculations.

containers

Collection of Dockerfiles

CRED-portal-v2

CWL

CWL Documents for commandlinetools and workflows

eclip-qc

maketrackhubs

metadata-db

Metadensity

Define metadensity to predict RNA binding protein function

Mudskipper

twenty-pelican-html5up

This is an adaptation of the html5up template "Twenty" for the Python static site generator Pelican.