LingyiC

besca_publication_results

FIST

singlecellvr

SPOTlight

Spatial Transcriptomics Capture Location Deconvolution

SPOTlight_deconvolution_analysis

single-cell-RNA-cluster

This is my final project for the Advanced Applied Statistics

SCmut

FastPG

Fast phenograph, CyTOF

shiny.rstudio.com-tutorial

Slides and exercises for the video tutorial at https://shiny.rstudio.com/tutorial/

SCHNAPPsContributions

some contributions to the scShinyHub project

pymi

Python implementation of mutual information calculation using B-spline from Daub et. al.

cafr

Attractor finding algorithm

scclusteval

Single Cell Cluster Evaluation

covid_balf

R script for the covid balf data analysis

vartrix

Single-Cell Genotyping Tool

scvelo

RNA Velocity generalized through dynamical modeling

cellranger-aws-pipeline-rebuild

scEpath

An energy landscape-based approach for measuring developmental states and inferring cellular trajectories from single cell RNA-seq data

DoubletDecon

A tool for removing doublets from single-cell RNA-seq data

GRNUlar

Gene Regulatory Network reconstruction using Unrolled algorithms

uncurl_app

scibet

A portable and fast single cell type identifier

SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

learning-bioinformatics-at-home

resources for learning bioinformatics

cheatsheets

Posit Cheat Sheets - Can also be found at https://posit.co/resources/cheatsheets/.

StemID

Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data.

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

MAPiT

MAPiT: measure-preserving MAP of pseudotime into true Time

HSNE-clustering

Scalable analysis of large high-dimensional data

pagoda2

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets