differential-gene-expression

There are 59 repositories under differential-gene-expression topic.

  • nanoporetech/pipeline-transcriptome-de

    Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

    Language:Python107213126

  • nuno-agostinho/psichomics

    Interactive R package to quantify, analyse and visualise alternative splicing

    Language:R36537911
  • workshop-RNAseq

    NBISweden/workshop-RNAseq

    Workshop • Analysis of RNA-seq data

    Language:CSS3442114

  • xzhoulab/iDEA

    Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

    Language:C++3253111

  • DeplanckeLab/ASAP

    ASAP : Automated Single-cell Analysis Pipeline

    Language:Java2471110
  • glmmSeq

    myles-lewis/glmmSeq

    Gene-level general linear mixed model

    Language:R1852410

  • wdecoster/DEA.R

    Script to automate differential expression analysis using DESeq2, edgeR or limma-voom

    Language:R17307

  • Kuanhao-Chao/RNASeqR

    📊 An R package of RNA-seq workflow

    Language:R15113

  • cemalley/scRNASeq-bulkRNASeq

    single cell and bulk RNASeq analysis scripts

    Language:HTML12229

  • pblumenkamp/GenExVis

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

    Language:Vue102880

  • csquires/dci

    Code and figures for the Differential Causal Inference (DCI) algorithm

    Language:Jupyter Notebook8501

  • pblumenkamp/Curare

    Curare - A customizable and reproducible analysis pipeline for RNA-Seq experiments

    Language:Python83381

  • kpatel427/DE_analysis

    Scripts to run differential expression analysis using DESeq2 package

    Language:R72010
  • fibrotime

    slowkow/fibrotime

    :tangerine: View the gene expression response to TNF and IL-17A with vanilla Javascript and HTML.

    Language:Jupyter Notebook7400

  • ben-laufer/RNA-seq

    RNA-seq alignment and analysis pipeline

    Language:R6104

  • breimanntools/xomics

    Python framework for explainable omics analysis

    Language:Jupyter Notebook6100

  • GrosseLab/VipeR_HIF1alpha

    Viper is a Snakemake workflow, aimed at performing the RNA-seq workflow of the paper 'Causes and consequences of a glutamine induced normoxic HIF1 activity for the tumor metabolism', Kappler et al. (2019) in a reproducible and automated manner

    Language:R6400
  • IgGeneUsage

    snaketron/IgGeneUsage

    Comparison of gene usage in immune repertoires under different biological conditions

    Language:R63131

  • DISC-IISR/RNAseqAnalysis

    The package RNAseqAnalysis does the complete analysis of RNA seq data starting from raw reads. It provides the user with differnt functions like generation of qc report, filtering, assembly and GO-term annotation, differential expression analysis and heatmap generation, and Alternative splicing-site prediction

    Language:R3101
  • dubportal

    labsyspharm/dubportal

    An integrative resource for deubiquitinating enzymes (DUBs) served at https://labsyspharm.github.io/dubportal

    Language:HTML3411

  • mppl1/RNAseq_preprocessing

    These are tutorials on a subset of tools available for processing raw RNAseq data. This if for HISAT2_SAMtools_Stringtie_gffcompare_ballgown pipeline or HISAT2_SAMtools_Stringtie_PrepDEanalysis.py_DESeq2 pipeline

    Language:Shell3200

  • TCP-Lab/bioTEA

    bioTEA - A user friendly tool to perform transcript expression analysis

    Language:Python30102

  • viktormiok/TempOseq_CarcinoChemMCF-7

    Cellular​ ​signatures​ characterisation ​after​ ​carcinogenic​ ​chemical​ ​exposure​ ​in​ ​mammalian​ ​tissue.

    Language:HTML3100

  • viktormiok/tigaR

    Temporal Integrative Genomics Analysis in R

    Language:R3101

  • Arnaroo/INDEGRA

    Accurate, easy and integrated suit to compare RNA samples with different degradation levels, quantify decay rates per-transcript and correct for degradation-induced artifacts in differential gene/transcript comparisons

    Language:Python200

  • bixBeta/DESeq2Shiny2

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

    Language:R210

  • csoderlund/TCW

    Analysis of single and comparative transcriptomes

    Language:Java2200

  • GrosseLab/BGSC

    Bayesian Gene Selection Criterion (BGSC) approach

    Language:R2200

  • JackXu2333/rseAnalysis

    An R package: RNA structure and Expression analysis

    Language:R2100

  • sbg/GENAVi

    Example R Shiny app demonstrating Seven Bridges Platform integration via OAuth2.

    Language:HTML220

  • YogiOnBioinformatics/Differential-Gene-Expression-Analysis-with-Machine-Learning-Using-Dexamethasone-Treatment-Data

    Worked with fellow peers at University of Pittsburgh under supervision of Dr. Junshu Bao, Department of Statistics, University of Pittsburgh, to do a Differential Gene Expression Analysis on a Dexamethasone treatment data set and incorporated Machine Learning into project.

    Language:R2102
  • SPresnell_GSE147507

    BenaroyaResearch/SPresnell_GSE147507

    GSE147507 SARS-Cov-2 Dataset from Mt. Sinai

    1602

  • cankocagil/BioStatistics

    Differential Gene Expression, Phylogenetic tree, Sequence Alignments, Biostatistics, Bioinformatic

    Language:R1100

  • DebmalyaSen34/Lasso-ElasticNet-regression-in-Lung-Cancer

    This repository contains a Jupyter Notebook for the analysis of Non-Small Cell Lung Cancer (NSCLC) data using various machine learning techniques.

    Language:Jupyter Notebook1100

  • genecell/Emergene

    Individual cell-based differential transcriptomic analysis across conditions

    Language:Python1100

  • JackXu2333/Reproducibility_Analysis_on_GIT

    Reproducibility Analysis on Genomic Impact Transformer (GIT)

    Language:Jupyter Notebook1100