differential-expression-analysis

There are 2 repositories under differential-expression-analysis topic.

• fgcz / prolfqua

  Differential Expression Analysis tool box R lang package for omics data

  proteomics-data-analysisrstats-packagehypothesis-testingquality-controlr-packagedifferential-expression-analysisprotein-quantification
  Language:R 36
• volcano3D

  KatrionaGoldmann / volcano3D

  An R package to plot interactive three-way differential expression analysis

  plotlyinteractivedifferential-expressiondifferential-expression-analysispackagevolcanoplotsbioinformaticscranomicstranscriptomicsgene-expressionrna-seq
  Language:HTML 31

• xinhe-lab / GSFA

  R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single-cell CRISPR screening data.

  single-cellcrispr-screen-analysisscrna-seq-analysisfactor-analysisdifferential-expression-analysis
  Language:C++ 16

• epigen / dea_limma

  A Snakemake workflow for performing and visualizing differential expression analyses (DEA) on NGS data powered by the R package limma.

  atac-seqbioinformaticsbiomedical-data-sciencechip-seqdifferential-expression-analysislimmalimma-trendlimma-voomrna-seqsnakemakevisualizationvolcano-plotworkflowscrna-seqstatisticsr
  Language:R 14

• epigen / dea_seurat

  A Snakemake workflow for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.

  bioinformaticsbiomedical-data-sciencedifferential-expression-analysisscrna-seqsingle-cellsnakemakesnrna-seqvisualizationworkflowvolcano-plot
  Language:R 10

• bharathananth / compareRhythms

  Approaches to identify Differential Rhythmicity

  rstatsr-packagehigh-throughput-data-analysiscircadian-rhythmsdifferential-expression-analysis
  Language:TeX 7

• OpenOmics / modr

  An awesome Oxford Nanopore Pipeline for direct RNA-sequencing

  direct-rna-sequencingoxford-nanoporerna-editingrna-modificationssingularitysnakemake-pipelinebioinformaticsnovel-transcriptspipelinequality-controltranscriptomicsknown-transcriptspolya-tail-length-estimationalternative-splicing-analysisdifferential-expression-analysis
  Language:Python 6

• shehio / Computational-Biology

  computational-biologysmith-watermansmith-waterman-alignmentgillespie-algorithmgillespiegradient-descentgradient-descent-algorithmgradient-descent-implementationgenome-analysisgenome-alignmentdifferential-analysisgene-expressionalternative-splicingdifferential-expressiondifferential-expression-analysissingle-cell-analysissingle-cell-genomicsviterbi-algorithmviterbi-decoderbowtie2
  Language:Jupyter Notebook 6

• pentalpha / r-peridot

  Software for intuitively doing Differential Gene Expression (DGE) analysis on Windows and GNU\Linux, based on R packages.

  differential-expressiondifferential-expression-analysisgene-expressionrna-seq-analysisrna-seq-pipelinebioinformaticsbioinformatics-pipelinebioconductorbioinformatics-analysisbioinformatics-tool
  Language:Java 4

• euxhenh / grinch

  A library for differential expression and gene set enrichment analysis based on hydra and pydantic.

  clusteringdifferential-expression-analysisgene-set-enrichmentmarker-genessingle-cellsingle-cell-analysis
  Language:Python 3

• jungsoh / transcriptomics-course

  Material used for a course on transcriptomics, covering transcriptome assembly, transcriptome functional annotation, differential expression analysis, and functional annotation data mining

  transcriptomicstranscriptome-assemblytranscriptome-annotationde-novo-assemblydifferential-expression-analysisfunctional-annotationannotation-data
  Language:HTML 3

• yotammarton / bioinformatics_course

  GWAS of Postmortem Brain Samples Sheds Light on the Development of Schizophrenia and Bipolar Disorder

  schizophreniabipolar-disordermapkgomafumiatbioindifferential-expression-analysispathway-enrichment-analysiswgcna
  Language:HTML 2

• MendenLab / miRNAInt_Ferroptosis

  Multi-omics differential expression and integration using PPI networks

  differential-expression-analysismultiomicsomics-data-integrationprotein-protein-interaction-network
  Language:R 1

• paulynamagana / Gene_Analysis

  Analysis of data from GEO

  differential-expression-analysisdna-methylationgene-analysis-algorithms
  Language:R 1

• sivkri / miRNASeq-DE-Analysis-QC

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

  deseq2deseq2-analysisdifferential-expression-analysisquality-controlrna-seqrna-seq-analysisrna-seq-datarna-seq-pipelinevisualization
  Language:R 1

• ATA82 / MotifSearcher

  Here, we describe and provide an RNA-Seq analysis of a RIP assay to understand the mechanism of AML del(9q) progression. (Ali T. Abdallah)

  amlaml-progressiondifferential-expression-analysisdeseq2motif-matchinghnrnp-ksequence-logos
  Language:R 0

• daniellakavanna / Transcriptomics-DE-Analysis

  Bioinformatics - Differential Expression Analysis

  bioinformaticsdifferential-expression-analysisexploratory-data-analysis
  Language:R 0

• EliasFarr / SPOT

  SPOT - Swift Profiling Of Transcriptomes - a shiny app for gene ranking according to user-defined expression profiles

  transcriptomicsshiny-appsexpressiongene-expressiongene-expression-profilesgene-rankingdifferential-expression-analysiseasy-to-usefast
  Language:R 0

• kirushka / ind_Tat_in_B_cells

  Differential gene expression and gene enrichment analyses of B-cell lines with stable and transient ectopic expression of HIV-1 Tat protein

  b-cell-lymphomadifferential-expression-analysisgseahiv-1
  Language:R 0

• programerkotik / Differential-Gene-Expression-Analysis

  Differential gene expression analysis exercise for the course Analytical Methods in Cancer Genomics 2023. The goal is to perform analysis of RNA-Seq data.

  differential-expression-analysisrna-seqrna-seq-analysis
  Language:R 0

• swiri021 / Difference_test_with_permutation

  Difference test with Gene expression by permutation method( by T-test and median test)

  genebioinformaticsttestdegdifferential-expression-analysis
  Language:Python 0

• swiri021 / NWPV2

  Method of Combined P-value to identify Differential Expressed Gene in dataset

  bioinformaticsdifferential-expression-analysisnwpvp-value
  Language:Python 0

• trinebera / N_oceanica_RNA-Seq_Analysis

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

  differential-expression-analysisrna-seqalgaedeseq2kallisto
  Language:Roff 0

• upendrabhattarai / denovo-RNA-Seq-On-Nesi

  This is a compilation of my scripts for denovo-RNA-Seq assembly, annotation, and get count metrics for Differential gene expression analysis in Nesi hpc.

  rna-seq-pipelinedenovo-assemblydifferential-expression-analysisnesi
  0

• abarrenos / EasyDEA

  EasyDEA: An Automated Tool for Differential Expression Analysis

  bioinformaticsdifferential-expression-analysisrna-seq
  Language:R

• Alejandro2195 / Differential-Expression-Analysis-in-R

  In this lab we will perform a differential expression analysis starting from scratch. Doxorubicin is a commonly prescribed cancer drug, but one of its side effects is cardiotoxicity. This drug damages heart cells by binding to the protein topoisomerase-II beta, or Top2b.

  bioconductorbioconductor-packagesbioinformaticsbiostatisticsdifferential-expressiondifferential-expression-analysisrstudio
  Language:HTML

• animesh / diffExpr

  R Shiny app for differential-expression analysis using T-test. The app is automatically deployed via GH Actions to shinyapp.io available as https://fuzzylife.shinyapps.io/diffExpr/

  proteomicsmassspectrometryttestdifferential-expression-analysis
  Language:R

• insilicolife / micti

  MICTI- Marker gene Identification for Cell Type Identity

  differential-expression-analysisfeature-extractionheterogeneous-cell-populationsmarker-genes
  Language:Jupyter Notebook

• kirushka / Tat_in_B_cells

  Differential gene expression and gene enrichment analyses of B-cell line with ectopic expression of HIV-1 Tat protein

  differential-expression-analysisgseahiv-1
  Language:R