deseq2

There are 93 repositories under deseq2 topic.

  • DGE_workshop

    Language:HTML360

  • Intro-to-R-with-DGE

    Language:R58

  • rna-seq-star-deseq2

    RNA-seq workflow using STAR and DESeq2

    Language:Python316
  • tidybulk

    tidybulk

    Brings bulk and pseudobulk transcriptomics to the tidyverse

    Language:R163

  • tximport

    Transcript quantification import for modular pipelines

    Language:R131

  • SARTools

    Statistical Analysis of RNA-Seq Tools

    Language:R103

  • differentialabundance

    Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

    Language:Nextflow46

  • recount

    R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/

    Language:R40

  • rnadeseq

    Differential gene expression analysis and pathway analysis of RNAseq data

    Language:Nextflow32

  • NASQAR

    NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization

    Language:HTML29

  • RNA-seq-tutorial-for-gene-differential-expression-analysis

    This tutorial is created for educational purpose

    Language:R28

  • deseq2_or_edger

    DESeq2 or edgeR

    Language:R22

  • deseq2shiny

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

    Language:R15

  • RNA-seq-differential-analyses-guideline

    A quick recap of widely used differential analyses methods in R for RNA-seq experiments

    12

  • DE_rpy2

    Differential expression analysis: DESeq2, edgeR, limma. Realized in python based on rpy2

    Language:Jupyter Notebook11

  • scRNASeq-bulkRNASeq

    single cell and bulk RNASeq analysis scripts

    Language:HTML10

  • GenExVis

    An application for exploring and visualizing differential gene expression data created with DESeq2

    Language:Vue9

  • R-scripts-graphing-statistics

    My R scripts, primarily R plotting scripts + some genomics software including 16S rRNA metataxnomics and RNAseq

    Language:R9

  • regionReport

    Generate HTML report for a set of genomic regions or DESeq2/edgeR results

    Language:R9

  • DE_analysis

    Scripts to run differential expression analysis using DESeq2 package

    Language:R7

  • Mcapitata_OA_Developmental_Gene_Expression_Timeseries

    Developmental timeseries of the reef-building coral Montipora capitata under predicted low and extreme low ocean acidification scenarios

    Language:HTML6

  • ppcseq

    Probabilistic outlier identification for bulk RNA sequencing data

    Language:R6

  • iBET

    interactive Bioinformatics Exploratory Tools

    Language:R5

  • Methods

    Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.

    Language:R5

  • Stony-Coral-Tissue-Loss-Disease-SCTLD-Project

    R scripts used for the analysis of microbiomes associated with stony coral tissue loss disease (SCTLD) in the Florida Reef Tract

    Language:R4

  • RNA-sequencing-analysis-in-R

    Analysis of RNA-seq data using DESeq2

    Language:R4

  • recountWorkflow

    Public repo for the recount Bioconductor workflow that is visible at http://bioconductor.org/help/workflows/

    Language:TeX4

  • pytximport

    A Python implementation of the `tximport` package.

    Language:Python3

  • BulkRNAseqAnalysis_from_countMatrix

    R Markdown script to perform bioinformatic analysis of RNA-seq raw count matrices, including DE-testing via DESeq2 and gene set enrichment analysis (GSEA).

    Language:R3

  • DESeq2-shiny

    A shiny application to perform differential gene expression analysis of count data using DESeq2. The app also allows unsupervised exploration of data using PCA and hierarchical clustering.

    Language:R3

  • nfkb-tag-seq

    Code for processing and analysis of TAGseq data in "The Effects of IKKβ Inhibition on Early NF-κB Activation and Transcription of Downstream Genes". Modified repository from https://github.com/z0on/tag-based_RNAseq.

    Language:R3

  • apoptosis_data_pipeline

    This repository houses the pipeline I coded to perform differential analysis of transcriptomes from two oyster species, C. gigas and C. virginica and isolate genes in the apoptosis pathway.

    Language:R3

  • 16S_Microbiome_Analysis

    This repository provides scripts for the 16S microbiome analysis and metagenome prediction using linux and R-Studio

    Language:Shell2

  • RNA-seq_Pipeline

    Deposited R scripts allow to execute a complete RNA-seq Pipeline, starting from sequence reads (FASTQ files) to mapping/annotate the genome using a reference, to counts the number of reads for every gene. when raw counts are obtained, DESeq2 module permits to find differentially expressed genes (DEG) and to perform statistical analysis. The last module of the project allows you to use clusterprofiler in order to perform ORA and GSEA analysis (over-representation analysis and gene set enrichment analysis) using GeneOntology (GO), disease ontology (DO), KEGG, reactome eg...

    Language:Jupyter Notebook2

  • UPF3

    Code and scripts for the RNA-seq analysis of project: Deciphering the cellular roles and dissecting functional regions of UPF3A and UPF3B in human NMD

    Language:R2
  • SMG5-SMG7

    SMG5-SMG7

    Code and scripts for the RNA-seq analysis of project: SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity

    Language:R2