deseq2

snakemake-workflows/rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

stemangiola/tidybulk

Brings bulk and pseudobulk transcriptomics to the tidyverse

thelovelab/tximport

Transcript quantification import for modular pipelines

PF2-pasteur-fr/SARTools

Statistical Analysis of RNA-Seq Tools

nf-core/differentialabundance

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

hbctraining/Intro-to-R-with-DGE

leekgroup/recount

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

qbic-pipelines/rnadeseq

Differential gene expression analysis and pathway analysis of RNAseq data

amarinderthind/RNA-seq-tutorial-for-gene-differential-expression-analysis

This RNAseq data analysis tutorial is created for educational purpose

nasqar/NASQAR

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

complextissue/pytximport

Feature-rich Python implementation of the tximport package for gene count estimation.

mikelove/deseq2_or_edger

DESeq2 or edgeR

nasqar/deseq2shiny

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

eonurk/RNA-seq-differential-analyses-guideline

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

cemalley/scRNASeq-bulkRNASeq

single cell and bulk RNASeq analysis scripts

peterlipan/DE_rpy2

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

pblumenkamp/GenExVis

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

raymondkiu/R-scripts-graphing-statistics

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

leekgroup/regionReport

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

echille/Mcapitata_OA_Developmental_Gene_Expression_Timeseries

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

kpatel427/DE_analysis

Scripts to run differential expression analysis using DESeq2 package

stemangiola/ppcseq

Probabilistic outlier identification for bulk RNA sequencing data

EmoryIntegratedComputationalCore/Methods

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

j-andrews7/iBET

interactive Bioinformatics Exploratory Tools

bixBeta/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.

LieberInstitute/recountWorkflow

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

meyermicrobiolab/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

shamitashetty/RNA-sequencing-analysis-in-R

Analysis of RNA-seq data using DESeq2

erinwitkop/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.

moritzmadern/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).

sachitsaksena/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.

bixBeta/DESeq2Shiny2

DESeq2Shiny2 is an R shiny application to handle NGS count data and perform unsupervised clustering and Differential Gene Expression Analysis using DESeq2.

boehmv/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

francescopatane96/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...

Zubair2021/16S_Microbiome_Analysis

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