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archrna

ArchR extension to analyze single cells transcriptome

cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor

cloops

Accurate and flexible loops calling tool for 3D genomic data.

cloops2

Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.

dotfiles

My dotfiles (macOS / Manjaro). My development environment setup (Java / Go / Rust). Configuration for vim / fish / zsh / i3 / tmux.

ericli0419.github.io

exfinder

Identifying external communication signals using single-cell transcriptomics data

hadge

Comprehensive pipeline for donor demultiplexing in single cell

higashi

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph

juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

ligand-receptor-pairs

Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.

ngs

Next-Gen Sequencing tools from the Horvath Lab

nichenetr

NicheNet: predict active ligand-target links between interacting cells

pando

Multiome GRN inference.

scale

SCANPY compatible version of SCALE

scalex

scevan

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

scomatic

A tool for detecting somatic variants in single cell data

scrabble

Perform Exploratory Computational Analyses on Processed Single-Cell RNA-Sequencing Data

scsparkl

scSPARKL is an Apache spark based pipeline for performing variety of preprocessing and downstream analysis of scRNA-seq data.

sequence_cnn_models

seurat-to-rna-velocity

A guide to using a Seurat object in conjunction with RNA Velocity

snaphic

SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data

somatic

space

stockquant

股票量化

tutorials