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flotilla
Reproducible machine learning analysis of gene expression and alternative splicing datasingle-cell-bioinformatics
Course material in notebook format for learning about single cell bioinformatics methodsclipper
A tool to identify CLIP-seq peaksoutrigger
Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq datasailor
CWL+Singularity implementation of an RNA editing workfloweCLIP
anchor
⚓ Find bimodal, unimodal, and multimodal features in your datarbp-maps
splicing and feature maps for RBPsqtools
qtools has helper functions to submit jobs to compute clusters (PBS on TSCC, SGE on oolite) from within Pythonsinglecell_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 alMINES
(m)6A (I)dentification Using (N)anopor(E) (S)equencinggscripts
General Use Scripts and Helper functionsExpedition
Expedition suite for computing, visualizing, and analyzing single-cell alternative splicing datamerge_peaks
Pipeline for using IDR to produce a set of peaks given two replicate eCLIP peaksbonvoyage
📐 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 dataBMS_bioinformatics_bootcamp_2017
repetitive-element-mapping
pipeline for mapping repetitive elementsFLARE
RNA edit detection (SAILOR) and peak calling (FLARE)cshl_2022
Collection of material to use for CSHL's Single Cell Analysis course 2022onboarding
Getting started in the yeolabYeo_STAMP_Nature_Methods
Code repository for "Robust single-cell discovery of RNA targets of RNA binding proteins and ribosome"MSTP_bioinformatics_bootcamp_2016
single-cell-bioinformatics-scrm-2016
Single cell bioinformatics class at the Sanford Consortium for Regenerative Medicine (SCRM) in 2016bodymap2
Flotilla package of Illumina bodymap datacshl_2019
Course materials for CSHL 2019peak-simulator
A tool to simulate CLIP-seq peakseclipdemux
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 pagesinglesail
A toolkit to help sail you through single-cell analysesCRaftID
software to accompany CRaftID paperhcp
Python port of Hierarchical Covariate with Prior from Matlab codeshalek2013
Dataset for Shalek et al 2013 single-cell analysis paperclip_analysis_legacy
PRINTER
Codebase used to generate analysis for PRINTER manuscript.chim-eCLIP
chimeric eCLIP processing pipelineSWIMMER
Statistical Workflow for Identification of Molecular Modulators of ribonucleoprotEins by Random variance modelingLove Open Source and this site? Check out how you can help us