deseq2
There are 93 repositories under deseq2 topic.
datasnakes/RNASeek
A shiny app to perform single and multifactor differential analysis using DESeq2, edgeR, and limma
jessmhoehner/Methods
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
nyuhuyang/RNAseq_pipeline
Pipeline of somatic variant analysis using Waldenstrom macroglobulinemia patient’s RNA-seq data, including tools like STAR, HTseq, VarScan in parallel computing in SGE clusters, Deseq2 and GSEA in R
svsuresh/rscripts
Repository miscellaneous R scripts including scripts for RNAseq analysis
tdayris-perso/rna-dge-salmon-deseq2
Perform differential analysis from FastQ files with Salmon, tximport, and DESeq2
aprezvykh/bioinformatics
some scripts to process transcriptomics and Chip-seq data
bissessk/RNA-seq-Analysis-of-Control-and-NRDE2-depleted-Breast-Cancer-Cells
Performed a differential gene expression analysis with RNA-seq that compares the expression in human control breast cancer cell lines with lines treated by silencing the NRDE2 gene. A Salmon + tximport + DESeq2 workflow was conducted to pursue this.
bixBeta/DESeq2Shiny2
DESeq2Shiny2 is an R shiny application to handle NGS count data and perform unsupervised clustering and Differential Gene Expression Analysis using DESeq2.
dgavr/Single_Cell_Iterative_Pooling
Iteratively randomly pooling scRNA-seq expressing a given gene from different numbers of cells and running DESeq2 with fdrtools correction to determine how many times which genes come out as enriched with said gene
Fjeanneret/multiSight
:bar_chart: :clipboard: Bioconductor R package with Graphical Interface to handle multi-omic data by Classification, Enrichment and Network inference.
LieberInstitute/recountWorkshop
Package for the recount workshop for BioC2017
PF2-pasteur-fr/SARTools-Galaxy
Galaxy wrappers for SARTools (Statistical Analysis of RNA-Seq Tools)
sivkri/miRNASeq-DE-Analysis-QC
Performing RNA-Seq data analysis and quality control using DESeq2 in R.
washingtoncandeia/kallisto_sleuth
Análise de RNA-seq - Abundância de Transcritos Utilizando kallisto, tximport e DESeq2
Alruta/Kallisto-DESeq2_Pipeline
A script to analyze with DESeq2 data from Kallisto. You maybe are interested only in DESeq2 part and its analisis and representation :)
DarkoCucin/nextflow-deseq2-repo
Nextflow implementation of DESeq2 for Seven Bridges CAVATICA platform
esharathgoud/Data-Analysis
linked with Bioinformatics analysis
foreverstas/DGE_workshop_rus
https://foreverstas.github.io/DGE_workshop_rus/
GwangWooKim/SBC-analysis
SBC analysis with DIGIST
HannahJeffery1/HannahJeffery1
Personalized, annotated code for anyone working with RNA-seq data.
kevincjnixon/autoDE
Automated DE analysis by DESeq2
lasamo/epimed_internship
Rstudio files created during my internship at IAB. Internship supervised by Florent Chuffart.
michalbukowski/aml-analysis
A collection of Jupyter notebooks for basic analysis of the data from the "BeatAML" study by Tyner et al. (2018)
michalbukowski/dge-ontology
Jupyter notebooks for DGE results and ontology analysis and visualisation.
michalbukowski/rnaseq-pipeline-2
Simple Nextflow RNA-Seq pipeline
OngMinXian/Differential-Expression-in-Stem-Cells-R-Shiny-Dashboard
A R shiny dashboard of differential expression in human embryonic stem cells.
raqmejtru/BCH339N_Predicting_Tumor_Phenotypes_from_Gene_Expression
We use gene expression data to perform gene set enrichments and random forest predictions to distinguish between four tumor types.
raqmejtru/mitonuclear-sd
Investigate the role of mtDNA in the sex determination/development of Potamilus streckersoni, a freshwater mussel with doubly uniparental mitochondrial inheritance. Scripts for DESeq2, WGCNA, GSEA, AlphaFold/AlphaPulldown, and mt-sncRNA validation.
rohan-b-84/dge_analysis_using_DESeq2
Differential Gene Expression analysis in R using DESeq2
roybarkan2020/Abalone-RNAseq-meta-analysis
Gene expression and network analysis for multiple RNA-seq datasets associated with heat-stress in abalone
Sam-Koehler/USDA-ARS-fusarium-community
R workflows used to analyze microbial community sequence data
tnation1392/BMB502FinalProject
Part of the final project for an Intro to Bioinformatics graduate course. Using RStudio I ran DESeq2 to show differentially expressed genes between control mice and mice infected with RSV.
trinebera/N_oceanica_RNA-Seq_Analysis
Differential gene expression analysis of Nannochloropsis oceanica growth with or without beneficial/harmful bacteria.
Anneser/zebrafishTelencephalon
Analysis code for scRNA-seq and bulk sequencing data from zebrafish telencephalon
safabio/modplots
Collection of customised plotting functions.
SUGAM2001/DESeq2-Python-Example
This repository contains an example implementation of DESeq2 in Python.