Codes for the scPLC project

STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

Supplemental code for "the architecture of SARS-CoV-2 transcriptome" paper

Cloud-based scalable and efficient single-cell genomics workflows

Draw phylogenetic trees of tumor evolution

A ggplot extension for drawing smooth non-convex circles around a set of points.

A Python-based EGA download client

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.

A tool set for short variant discovery in genetic sequence data.

A tool for detecting somatic variants in single cell data

Python package to annotate and visualize gene fusions.

The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This algorithm also works in bulk expression profiling data.)

An awesome R-shiny list!

shinyWidgets : Extend widgets available in shiny

R Shiny apps

Somatic variant calling tools for RNAseq data

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

Clone identification from single-cell data

Clustering scRNAseq by genotypes

scRNAseq analysis notes from Ming Tang

Utilities repository to analyze single-cell data from https://www.nature.com/articles/s41467-018-07261-3.