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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
β 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
β¨ 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 functionsmerge_peaks
Pipeline for using IDR to produce a set of peaks given two replicate eCLIP peaksbonvoyage
π 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 2019makebigwigfiles
Converts a BAM file into strand-specific bigwig files.peak-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