Yini-Li's repositories
jvarkit
Java utilities for Bioinformatics
dynamo-release
Inclusive model of expression dynamics with metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
guideseq
Analysis pipeline for the GUIDE-seq assay. For news, see:
MeDIP-seq
A set of scripts and functions for analyzing MeDIP-seq datasets
scNT-seq
Data analysis pipeline for scNT-seq (single-cell metabolically labeled new RNA tagging sequencing)
Detect-seq
An unbiased method for genome-wide CBE off-targets assessment
beautiful-jekyll
:sparkles: Build a beautiful and simple website in literally minutes. Demo at https://beautifuljekyll.com
zUMIs
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
Smart-seq3
Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).
exomePeak
Analysis of RNA epitranscriptome sequencing data with affinity-based shotgun sequencing approach
txburst
Transcriptional burst kinetics inference and analysis described in the article "Genomic encoding of transcriptional burst kinetics" by Anton J. M. Larsson, Per Johnsson, Michael Hagemann-Jensen, Leonard Hartmanis, Omid R. Faridani, Björn Reinius, Åsa Segerstolpe, Chloe M. Rivera, Bing Ren and Rickard Sandberg
merip_reanalysis_scripts
Scripts for paper entitled "Limits in the detection of m6A changes using MeRIP/m6A-seq
EPIMAP_ANALYSIS
Epimap processing and analysis code repository
MatchedFilter
Prediction of Active Enhancers and Promoters in a Cell type specific manner using shape matching of histone and/or DNase-I hypersensitivity profiles
cardips-ipsc-eqtl
CARDIPS iPSC eQTL study.
crisporPaper
Code for the CRISPOR article, all data and code to create figures and analysis