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#

bulk-rna-seq

Here are 49 public repositories matching this topic...

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

  • UpdatedMar 16, 2025
  • Jupyter Notebook

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

  • UpdatedMar 28, 2024
  • R

🌺 reference-free transcriptome assembly for short and long reads

  • UpdatedJan 28, 2024
  • Java

a fully Bayesian approach to deconvolve tumor microenvironment

  • UpdatedJun 20, 2022
  • R

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

  • UpdatedJun 14, 2024
  • Python

Workflow management with Nextflow and nf-core

  • UpdatedJan 21, 2025
  • Nextflow

Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor

  • UpdatedFeb 4, 2025
  • R

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

  • UpdatedOct 21, 2024
  • R

GenoCraft: A Comprehensive, User-Friendly Web Platform for High-Throughput Omics Data Analysis and Visualization (https://arxiv.org/pdf/2312.14249)

  • UpdatedOct 29, 2024
  • SCSS

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

  • UpdatedApr 19, 2020
  • R

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.

  • UpdatedMar 18, 2025
  • Jupyter Notebook

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

  • UpdatedDec 8, 2024
  • R

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

  • UpdatedSep 30, 2024
  • Groovy

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

  • UpdatedJul 18, 2023
  • Jupyter Notebook

Trajectory Inference of clinical data via Multi-commodity Flow

  • UpdatedJul 4, 2024
  • Jupyter Notebook

Analysis pipeline for bulk RNA-seq data

  • UpdatedAug 18, 2022
  • Python

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

  • UpdatedMay 27, 2022
  • Shell

An R tool to detect and correct batch-effects in gene-expression data (Microarray and bulk-RNAseq))

  • UpdatedJan 7, 2023
  • R

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