deseq2

There are 92 repositories under deseq2 topic.

  • NBayTNCoystersAnalysis

    Scripts for analysis of metatranscriptomic and 16S rRNA amplicon data from wild oysters in Narragansett Bay

    Language:R2

  • rna-dge-salmon-deseq2

    Perform differential analysis from FastQ files with Salmon, tximport, and DESeq2

    Language:Python2

  • Methods

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

    Language:R2

  • rscripts

    Repository miscellaneous R scripts including scripts for RNAseq analysis

    Language:Jupyter Notebook2

  • RNASeek

    A shiny app to perform single and multifactor differential analysis using DESeq2, edgeR, and limma

    Language:HTML2

  • 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

    Language:HTML2

  • DESeq2Shiny2

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

    Language:R1

  • miRNASeq-DE-Analysis-QC

    Performing RNA-Seq data analysis and quality control using DESeq2 in R.

    Language:R1

  • multiSight

    :bar_chart: :clipboard: Bioconductor R package with Graphical Interface to handle multi-omic data by Classification, Enrichment and Network inference.

    Language:R1

  • 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.

    Language:Shell1

  • 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

    Language:Python1

  • kallisto_sleuth

    Análise de RNA-seq - Abundância de Transcritos Utilizando kallisto, tximport e DESeq2

    Language:R1

  • bioinformatics

    some scripts to process transcriptomics and Chip-seq data

    Language:R1

  • recountWorkshop

    Package for the recount workshop for BioC2017

    Language:HTML1

  • SARTools-Galaxy

    Galaxy wrappers for SARTools (Statistical Analysis of RNA-Seq Tools)

    Language:R1

  • dge_analysis_using_DESeq2

    Differential Gene Expression analysis in R using DESeq2

    Language:HTML

  • zebrafishTelencephalon

    Analysis code for scRNA-seq and bulk sequencing data from zebrafish telencephalon

    Language:Jupyter Notebook

  • aml-analysis

    A collection of Jupyter notebooks for basic analysis of the data from the "BeatAML" study by Tyner et al. (2018)

    Language:Jupyter Notebook

  • nextflow-deseq2-repo

    Nextflow implementation of DESeq2 for Seven Bridges CAVATICA platform

    Language:R

  • 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.

    Language:R
  • mitonuclear-sd

    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.

    Language:R

  • SBC-analysis

    SBC analysis with DIGIST

    Language:R

  • Differential-Expression-in-Stem-Cells-R-Shiny-Dashboard

    A R shiny dashboard of differential expression in human embryonic stem cells.

    Language:R

  • dge-ontology

    Jupyter notebooks for DGE results and ontology analysis and visualisation.

    Language:Jupyter Notebook

  • 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.

  • rnaseq-pipeline-2

    Simple Nextflow RNA-Seq pipeline

    Language:Nextflow

  • modplots

    Collection of customised plotting functions.

    Language:R

  • 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 :)

  • Abalone-RNAseq-meta-analysis

    Gene expression and network analysis for multiple RNA-seq datasets associated with heat-stress in abalone

  • epimed_internship

    Rstudio files created during my internship at IAB. Internship supervised by Florent Chuffart.

    Language:R

  • Data-Analysis

    linked with Bioinformatics analysis

    Language:Shell

  • N_oceanica_RNA-Seq_Analysis

    Differential gene expression analysis of Nannochloropsis oceanica growth with or without beneficial/harmful bacteria.

    Language:Roff

  • HannahJeffery1

    Personalized, annotated code for anyone working with RNA-seq data.

    Language:R

  • autoDE

    Automated DE analysis by DESeq2

    Language:R

  • DGE_workshop_rus

    https://foreverstas.github.io/DGE_workshop_rus/

    Language:HTML

  • USDA-ARS-fusarium-community

    R workflows used to analyze microbial community sequence data

    Language:R