YeoLab/BMS_bioinformatics_bootcamp_2017

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YeoLab/BMS_bioinformatics_bootcamp_2017

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flotilla

Reproducible machine learning analysis of gene expression and alternative splicing data

Jupyter Notebook

single-cell-bioinformatics

Course material in notebook format for learning about single cell bioinformatics methods

Jupyter Notebook

clipper

A tool to identify CLIP-seq peaks

outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data

sailor

CWL+Singularity implementation of an RNA editing workflow

Jupyter Notebook

eCLIP

Common Workflow Language

anchor

⚓ Find bimodal, unimodal, and multimodal features in your data

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

singlecell_pnm

✨ Code and figures accompanying the paper, "Single-cell alternative splicing analysis with Expedition reveals splicing dynamics during neuron differentiation" by Song and Botvinnik, et al

Jupyter Notebook

MINES

(m)6A (I)dentification Using (N)anopor(E) (S)equencing

gscripts

General Use Scripts and Helper functions

Expedition

Expedition suite for computing, visualizing, and analyzing single-cell alternative splicing data

merge_peaks

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

bonvoyage

📐 Transform percentage-based units into a 2d space to evaluate changes in distribution with both magnitude and direction.

skipper

Skip the peaks and expose RNA-binding in CLIP data

repetitive-element-mapping

pipeline for mapping repetitive elements

FLARE

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

cshl_2022

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

Jupyter Notebook

onboarding

Getting started in the yeolab

Yeo_STAMP_Nature_Methods

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

Jupyter Notebook

MSTP_bioinformatics_bootcamp_2016

Jupyter Notebook

single-cell-bioinformatics-scrm-2016

Single cell bioinformatics class at the Sanford Consortium for Regenerative Medicine (SCRM) in 2016

Jupyter Notebook

bodymap2

Flotilla package of Illumina bodymap data

cshl_2019

Course materials for CSHL 2019

Jupyter Notebook

makebigwigfiles

Converts a BAM file into strand-specific bigwig files.

peak-simulator

A tool to simulate CLIP-seq peaks

eclipdemux

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

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

singlesail

A toolkit to help sail you through single-cell analyses

CRaftID

software to accompany CRaftID paper

Jupyter Notebook

hcp

Python port of Hierarchical Covariate with Prior from Matlab code

shalek2013

Dataset for Shalek et al 2013 single-cell analysis paper

clip_analysis_legacy

PRINTER

Codebase used to generate analysis for PRINTER manuscript.

Jupyter Notebook

chim-eCLIP

chimeric eCLIP processing pipeline

Common Workflow Language

SWIMMER

Statistical Workflow for Identification of Molecular Modulators of ribonucleoprotEins by Random variance modeling

Jupyter Notebook