transcriptomics 开源项目推荐（1,289 个）

scverse /scanpy

Python中的单细胞分析。扩展至> 1亿个细胞。

scverse /gget

Glugget能够高效查询基因组参考数据库

instadeepai /nucleotide-transformer

Foundation Models for Genomics & Transcriptomics

chanzuckerberg /cellxgene

An interactive explorer for single-cell transcriptomics data

scverse /anndata

Annotated data.

scverse /PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

aertslab /pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

theislab /scgen

Single cell perturbation prediction

mahmoodlab /PathomicFusion

Fusing Histology and Genomics via Deep Learning - IEEE TMI

scverse /decoupler

Python package to perform enrichment analysis from omics data.

opencobra /cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

GoekeLab /bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

kharchenkolab /pagoda2

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

spacetx /starfish

starfish: unified pipelines for image-based transcriptomics

keller-mark /awesome-biological-visualizations

A list of web-based interactive biological data visualizations.

ZJUFanLab /scCATCH

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

ablab /IsoQuant

A universal toolkit for upstream processing of long RNA reads

iSEE /iSEE

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

COMBINE-lab /alevin-fry

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

obophenotype /cell-ontology

An ontology of cell types