Pinned Repositories
10x-scATAC-2019
Publication Page for Satpathy*, Granja* et al 2019
2019_Strunz
Reproducibility repo accompanying Angelidis et al. "Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration"
adv-r
Advanced R: a book
advanced-shiny
Shiny tips & tricks for improving your apps and solving common problems
AmpUMI
Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
ATAC-pipe
Analysis pipeline for ATAC-seq Data
atac-seq-pipeline
ENCODE ATAC-seq pipeline
ATAC_mito_sc
single cell ATACseq pipeline
awesome-10x-genomics
List of tools and resources related to the 10x Genomics GEMCode/Chromium system
awesome-single-cell
List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
MichaelZH24's Repositories
MichaelZH24/10x-scATAC-2019
Publication Page for Satpathy*, Granja* et al 2019
MichaelZH24/AmpUMI
Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
MichaelZH24/Bioinformatics
Bioinformatics Workflows
MichaelZH24/bpipes
bioinformatic pipelines
MichaelZH24/c9-python-getting-started
Sample code for Channel 9 Python for Beginners course
MichaelZH24/ChIP-seq-analysis
ChIP-seq analysis notes from Ming Tang
MichaelZH24/CLiNC
MichaelZH24/coursera-ml-py
Python programming assignments for Machine Learning by Prof. Andrew Ng in Coursera
MichaelZH24/CRISPResso2
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
MichaelZH24/Custom_CARLIN
MichaelZH24/dropseqRunner
Pipeline for processing single-cell RNA-seq data (drop-seq)
MichaelZH24/eoulsan
A pipeline and a framework for NGS analysis (RNA-Seq and soon Chip-Seq)
MichaelZH24/lab-website-template
An easy-to-use, flexible website template for labs!
MichaelZH24/longread_umi
MichaelZH24/markdown_photo
MichaelZH24/MIPGEN
One stop MIP design and analysis
MichaelZH24/mlcourse.ai
Open Machine Learning Course
MichaelZH24/Pfirschke_et_al_2021
MichaelZH24/pyprobml
Python code for "Machine learning: a probabilistic perspective" (2nd edition)
MichaelZH24/pySCENIC-test
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
MichaelZH24/PythonSIFT
A clean and concise Python implementation of SIFT (Scale-Invariant Feature Transform)
MichaelZH24/scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
MichaelZH24/SCENICprotocol
A scalable SCENIC workflow for single-cell gene regulatory network analysis
MichaelZH24/SelfTarget
Scripts for processing and predicting CRISPR/Cas9-generated mutations
MichaelZH24/single-cell-tutorial
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
MichaelZH24/singlecell-qtl
MichaelZH24/SingleCellLineage
Updated scripts and pipelines for processing GESTALT data at single-cell resolution
MichaelZH24/snakemake_DARLIN
MichaelZH24/tinyatlas
A tiny cell atlas for commonly sequenced organisms.
MichaelZH24/udlbook
Understanding Deep Learning - Simon J.D. Prince