Ruismart

URD

URD - Reconstruction of Branching Developmental Trajectories

GLUE

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

MeDuSA

MeDuSA is a fine-resolution cellular deconvolution method that leverages scRNA-seq data as a reference to estimate cell-state abundance in bulk RNA-seq data.

kdm6b

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

ShinyCell

Shiny Interactive Web Apps for Single-Cell Data

scg_lib_structs

Collections of library structure and sequence of popular single cell genomic methods

scvelo

RNA Velocity generalized through dynamical modeling

scanpy

Single-cell analysis in Python. Scales to >1M cells.

seurat-wrappers

Community-provided extensions to Seurat

GSEApy

Gene Set Enrichment Analysis in Python

Th17_single_cell

2021_NI_scGCB

Code for analysis of scGCB paper

ChIPseeker

:dart: ChIP peak Annotation, Comparison and Visualization

demultiplex

Versatile FASTA/FASTQ demultiplexer.

MACS

MACS -- Model-based Analysis of ChIP-Seq

clust

Automatic and optimised consensus clustering of one or more heterogeneous datasets

zju-icicles

浙江大学课程攻略共享计划

REKCARC-TSC-UHT

清华大学计算机系课程攻略 Guidance for courses in Department of Computer Science and Technology, Tsinghua University

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

scDEC

Simultaneous deep generative modeling and clustering of single cell genomic data

scPred

scPred package for cell type prediction from scRNA-seq data

scrublet

Detect doublets in single-cell RNA-seq data

DoubletFinder

R package for detecting doublets in single-cell RNA sequencing data

copykat

scRNA_GBM

analysis script for GBM single cell RNA seq data

CONICS

CONICS: COpy-Number analysis In single-Cell RNA-Sequencing

TCR-BCR-seq-analysis

T/B cell receptor sequencing analysis notes

immunarch

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires