Yeo lab at UCSD

single-cell-bioinformatics

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

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

anchor

:anchor: Find bimodal, unimodal, and multimodal features in your data

singlecell_pnm

:sparkles: 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

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

BMS_bioinformatics_bootcamp_2017

bonvoyage

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

onboarding

Getting started in the yeolab

MSTP_bioinformatics_bootcamp_2016

single-cell-bioinformatics-scrm-2016

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

bodymap2

Flotilla package of Illumina bodymap data

cshl_2019

Course materials for CSHL 2019

makebigwigfiles

Converts a BAM file into strand-specific bigwig files.

CRaftID

software to accompany CRaftID paper

hcp

Python port of Hierarchical Covariate with Prior from Matlab code

shalek2013

Dataset for Shalek et al 2013 single-cell analysis paper

singlesail

A toolkit to help sail you through single-cell analyses

SWIMMER

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

cookiecutter-pypackage

Cookiecutter template for a Python package. See https://github.com/audreyr/cookiecutter.

f-SHAPE-eCLIP

Generate fSHAPE/SHAPE reactivity profiles from (f)SHAPE-eCLIP reads.

flotilla_test_data

scrambled data for testing flotilla functionality

fSHAPE

Generate fSHAPE reactivity profiles from in vivo/in vitro SHAPE probing reads.

PyCharm-Python-Templates

Python Templates for the PyCharm IDE

region_based_CLIP_enrichment

pipeline for region-based enrichment based on Eric's methods

spectrum-of-differentiation-supplements

Mirror of analysis files for "Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells"

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

toil

A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python