GGCAQinChao

COPILOT

Single cell RNA-seq preprocessing tool for gene-by-cell matrices of UMI counts. It is recommended to use the raw spliced and unpliced counts matrices produced by scKB pipeline as the input of copilot.

CellNeighborEX

CellNeighborEX: Deciphering Neighbor-Dependent Gene Expression from Spatial Transcriptomics Data

EAGS

EAGS:efficient and adaptive Gaussian smoothing

scPred

scPred package for cell type prediction from scRNA-seq data

celltypist

A tool for semi-automatic cell type classification

cellassign

Automated, probabilistic assignment of cell types in scRNA-seq data

DNBelab_C_Series_scRNA-analysis-software

An open source and flexible pipeline to analyze DNBelab C Series single-cell RNA datasets.

TOSICA

Transformer for One-Stop Interpretable Cell-type Annotation

infercnv

Inferring CNV from Single-Cell RNA-Seq

SCmut

Guideline-for-Computational-Biology-and-Bioinformatics

cellhint

A tool for semi-automatic cell type harmonization and integration

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

GNTD

Reconstructing Spatial Transcriptomes with Graph-guided Neural Tensor Decomposition Informed by Spatial and Functional Relations

scrattch.bigcat

iterative clustering pipeline of big single cell datasets.

SEDR

STAligner

STAligner is a tool for alignment and integration of spatially resolved transcriptomics data.

SCDC

SCDC

bisque

An R toolkit for estimation of cell composition from bulk expression data

bulk2space

a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles

deconv_matching_bulk_scnRNA

Repository for "Effective methods for bulk RNA-seq deconvolution using scRNA-seq and snRNA-seq derived transcriptomes"

SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

STAGATE

Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics

torchdrug

A powerful and flexible machine learning platform for drug discovery

spaTrack

stLearn

A novel machine learning pipeline to analyse spatial transcriptomics data

SLAT

Spatial-Linked Alignment Tool

DeepCCI

16GT

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html