hengbingao

SCpubr_Rlike_scanpy

Generate high quality, publication ready visualizations for single cell transcriptomics data.

cNMF_elif_removebatch

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

TOBIAS_ATAC_footprint

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

snATAC_NMF_EricYangLi

SnapATAC2

Single-cell epigenomics analysis tools

MethSCAn_snMethylation

Python package with CLI for downstream analysis of single cell methylation data.

pytorch_machine-learning

Tensors and Dynamic neural networks in Python with strong GPU acceleration

GLUE_tools

Graph-linked unified embedding for single-cell multi-omics data integration

CellSpace

Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace

mouse_brain_transcript

iterative clustering pipeline of big single cell datasets.

LanXuan_scATAC_Rcode

小鼠染色质可及性图谱，使用R进行分析的全套pipelines

mouse_brain_scRNA

Genearlized mapping scripts for RNA-seq and Patch-seq data

TFvelo

sciMETv2

LiYangEric_science2023_binglab

cisDynet_bulkATAC_RNAseq

An integrated platform for modeling gene-regulatory dynamics and networks

brain-enhancer

plot1cell

ATAC-seq

Analysis pipeline for ATAC-seq data

Kaya-ListerLab-Tutorial

Info about how to setup, use and work on UWA's Kaya system. Includes a tutorial with example code

sklearn-doc-zh

:book: [译] scikit-learn（sklearn） 中文文档

cpgtools

Python package to analyze DNA methylation data

SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

wmb2023_Hanqing-Liu

Code and data sharing of Liu et al. 2023 manuscript

ArchR_snATAC_snRNA

jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

EDTA

Extensive de-novo TE Annotator

GWAS_grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.

Taiji_pagerank_GRN_TF

All-in-one analysis pipeline

JASPAR-UCSC-tracks

Code and data used to create the JASPAR UCSC Genome Browser tracks data hub