bulk-rna-seq 开源项目推荐（124 个）

omicverse /omicverse

用于多组学的Python库包括批量、单细胞和空间RN-seq分析。

digitalcytometry /ecotyper

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.

BirolLab /RNA-Bloom

🌺 reference-free transcriptome assembly for short and long reads

nunofonseca /irap

integrated RNA-seq Analysis Pipeline

earmingol /cell2cell

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

Danko-Lab /TED

a fully Bayesian approach to deconvolve tumor microenvironment

carpentries-incubator /workflows-nextflow

Workflow management with Nextflow and nf-core

carpentries-incubator /bioc-rnaseq

Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor

IGS /gEAR

The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.

hms-dbmi /dseqr

single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.

AyehBlk /RAPTOR

RNA-seq Analysis Pipeline Testing and Optimization Resource - Intelligent pipeline selection and comprehensive benchmarking.

futianfan /GenoCraft

GenoCraft：一个全面且用户友好的 Web 平台，用于高通量组学数据分析与可视化（https://arxiv.org/pdf/2312.14249）

luuloi /AppliedBioinformatics2023

"Applied bioinformatics" is a course for Genetics Master Program at Genetics Department

cemalley /scRNASeq-bulkRNASeq

single cell and bulk RNASeq analysis scripts

nasqar /deseq2shiny

a web-based R shiny application that wraps DESeq2 R package

NUPulmonary /2020_Grant

Code base for the Grant, Morales-Nebreda, and Markov et al., “Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia” Nature (2021) paper

dalmolingroup /bulkrna

Dalmolin Group's workflow for pre-processing, alignment and quantification of bulk RNA-seq data

euxhenh /Truffle

Trajectory Inference of clinical data via Multi-commodity Flow

jalwillcox /Calculate-PSI

A script used to calculate percent spliced-in (PSI) values from bulk RNA sequencing data.

nygenome /DECONVersation

DECONVersation deconvolves bulk RNA-seq data using embeddings from large-scale, LLM-based foundation models.