Shicheng Guo's Projects
SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
Tools (written in C using htslib) for manipulating next-generation sequencing data
scripts and notebooks from sanbomics
Deep mutational scanning of the receptor-binding domain of SARS-CoV-2 Spike
Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding
Survey of ACE2 binding specificities among SARS-related CoV homologs
Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space
:exclamation: This is a read-only mirror of the CRAN R package repository. scatterPlotMatrix — 'Htmlwidget' for a Scatter Plot Matrix. Homepage: https://ifpen.gitlabfr.com/detocs/scatterplotmatrix Report bugs for this package: https://ifpen.gitlabfr.com/detocs/scatterplotmatrix/-/issues
scDCC: Single Cell Deep Constrained Clustering
R package for analyzing single-cell RNA-seq data
scDeepCluster for Single Cell RNA-seq data
Single-cell disease relevance score (scDRS)
Analyse citation data from Google Scholar
A parser for Google Scholar, written in Python
An idea comes into my mind. To illustrate social network of scientists using R.
scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning
scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources of variation.
Functions for web scraping
Scripts from the Joung et al Nature Protocols 2016 manuscript on knockout and transcriptional activation screening
Comprehensive Analysis of the Expression of N6-Methyladenosine RNA Methylation Regulators in Pulmonary Artery Hypertension
Single-Cell Transcriptome Analysis Reveals Inter-Tumor Heterogeneity in Bilateral Papillary Thyroid Carcinoma
shiny app for single cell RNAseq experiments, with plug-in like structure for flexible integration of tools and visualizations.
RNA Velocity generalized through dynamical modeling
Deep probabilistic analysis of single-cell omics data