differential-expression

There are 4 repositories under differential-expression topic.

owkin / PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
bioinformatics differential-expression python rna-seq transcriptomics
Language:Python 695
dmcable / spacexr
Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
cell-type-identification differential-expression spatial-transcriptomics
Language:HTML 408
theislab / diffxpy
Differential expression analysis for single-cell RNA-seq data.
differential-expression single-cell-rna-seq gene-set-enrichment bioinformatics transcriptomics tensorflow
Language:Python 204
tidybulk
stemangiola / tidybulk
Brings bulk and pseudobulk transcriptomics to the tidyverse
tidyverse tidy tidy-data bioconductor edger deseq2 transcriptomics pipe tibble gene-symbols bulk-transcriptional-analyses mds-dimensions ensembl-ids transcripts tsne pca redundancy entrez gsea differential-expression
Language:R 173
saeyslab / multinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
cell-cell-communication differential-expression intercellular-communication intercellular-signaling ligand-receptor ligand-receptor-interaction ligand-target scrna-seq single-cell single-cell-rna-seq systems-biology cell-cell-interaction
Language:HTML 167
parashardhapola / scarf
Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.
bioinformatics single-cell-genomics single-cell-rna-seq dimension-reduction clustering umap tsne big-data cite-seq single-cell-atac-seq memory-efficient scalable-data-analysis scrna-seq scatac-seq pseudotime multiomics gene-modules differential-expression graph-analytics genomics
Language:Python 108
nf-core / differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
nextflow nf-core pipeline workflow atac-seq chip-seq deseq2 differential-abundance differential-expression gsea limma microarray rna-seq shiny
Language:Nextflow 84
nunofonseca / irap
integrated RNA-seq Analysis Pipeline
irap pipeline rna-seq-analysis rna-seq gene-expression transcript-quantification bulk-rna-seq single-cell-rna-seq exon-quantification differential-expression
Language:R 84
SCPA
jackbibby1 / SCPA
R package for pathway analysis in scRNA-seq data
single-cell pathway-analysis differential-expression gene-signatures r-package single-cell-rna-seq transcriptomics
Language:R 75
snakemake-workflows / rna-seq-kallisto-sleuth
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
snakemake kallisto sleuth rna-seq differential-expression sciworkflows reproducibility
Language:Python 68
wckdouglas / diffexpr
Porting DESeq2 into python via rpy2
rna-seq python differential-expression
Language:Python 68
Russel88 / DAtest
Compare different differential abundance and expression methods
microbiome rnaseq relative-abundances compare-methods differential-abundance-methods otu marker-gene-analysis 16s proteomics metabolomics metagenomics differential-expression auc false-positive-control
Language:R 52
BaderLab / scClustViz
Explore and share your scRNAseq clustering results
r ui scrna-seq scrnaseq scrna-seq-analysis single-cell shiny differential-expression clustering-evaluation
Language:R 50
heiniglab / scPower
Experimental design framework for scRNAseq population studies (eQTL and DE)
differential-expression eqtl power-analysis single-cell
Language:R 46
grimmlab / BookChapter-RNA-Seq-Analyses
Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq analysis
bioinformatics differential-expression pipeline rnaseq-analysis
Language:Shell 40
volcano3D
KatrionaGoldmann / volcano3D
An R package to plot interactive three-way differential expression analysis
plotly interactive differential-expression differential-expression-analysis package volcanoplots bioinformatics cran omics transcriptomics gene-expression rna-seq
Language:HTML 38
mritchielab / GlimmaV2
interactive plots for differential expression analysis
differential-expression r interactive-visualizations
Language:JavaScript 34
nf-core / lncpipe
UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
lncrna rna-seq-analysis transcriptome differential-expression nf-core nextflow workflow pipeline rna long-non-coding non-coding
Language:Nextflow 34
noamteyssier / adpbulk
pseudobulking on an AnnData object
anndata differential-expression pseudobulk scanpy
Language:Python 34
federicomarini / ideal
Interactive Differential Expression AnaLysis - DE made accessible and reproducible
bioconductor differential-expression r reproducible-research rna-seq rna-seq-analysis shiny user-friendly
Language:R 31
himelmallick / Tweedieverse
Differential analysis of multi-omics data based on the Tweedie distribution
differential-abundance-analysis differential-expression metagenomics microbiome multi-omics-data single-cell
Language:R 28
theislab / batchglm
Fit generalized linear models in python.
generalized-linear-models tensorflow differential-expression
Language:Python 28
DeplanckeLab / ASAP
ASAP : Automated Single-cell Analysis Pipeline
asap bioinformatics bioinformatics-pipeline clustering differential-expression differential-gene-expression enrichment filtering gene-expression normalization ontology pca rna-seq single-cell t-sne transcriptomics visualization web-app web-application web-tool
27
lpantano / DEGreport
Create a cromphensive report of DEG list coming from any analysis of RNAseq data
r bioconductor rna-seq smallrna report qc differential-expression
Language:R 26
stemangiola / bioc_2020_tidytranscriptomics
Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap
tidyverse differential-expression tidybulk heatmap pca mds transcriptomics tidy-data bioconductor r bioc2020 workshop
Language:R 26
refinery-platform / heatmap-scatter-dash
Interactive visualizations for differential expression
visualization refinery docker differential-expression
Language:Python 25
Bohdan-Khomtchouk / Microscope
ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps
chip-seq rna-seq heatmap gene-ontology principal-component-analysis differential-expression network-analysis gene-expression computational-biology r-programming statistical-analysis
Language:R 23
olgatsiouri1996 / biomisc_R
command line bioinformatic scripts written in R
bioinformatics differential-expression fasta r statistics
Language:R 23
shao-lab / MAnorm
A robust model for quantitative comparison of ChIP-Seq data sets.
bioinformatics chip-seq normalization differential-expression ngs
Language:Python 23
hemberg-lab / D3E
Discrete Distributional Differential Expression
differential-expression single-cell-rna-seq human-cell-atlas
Language:Python 22
allielarocco / Microarray-Analysis
Microarray Analysis Pipeline in Python
microarray microarray-studies microarray-experiments pipeline enrichment-analysis differential-expression differentially-expressed-genes ncbi-geo ncbi-database ncbi-submission
Language:Jupyter Notebook 19
btmonier / vidger
Make rapid visualizations of RNA-seq data in R
data-munging differential-expression gene-expression r rna-seq-analysis visualization
Language:R 19
fperraudeau / singlecellworkflow
Tutorial for the analysis of scRNA-seq data in R
bioconductor clustering differential-expression dimensionality-reduction lineage normalization r single-cell single-cell-rna-seq workflow
Language:TeX 18
lingfeiwang / normalisr
Causal inference, differential expression, and co-expression for scRNA-seq
association-testing causal-inference co-expression differential-expression gene-regulatory-network hypothesis-testing normalization scrna-seq single-cell single-cell-crispr-screening
Language:Python 18
sanjaynagi / rna-seq-pop
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
snakemake-workflow rna-seq variant-calling differential-expression population-genomics snakemake transcriptomics workflow population-genetics selection karyotype ancestry genomic-surveillance
Language:Jupyter Notebook 18
tucca-cellag / tucca-rna-seq
TUCCA's RNA-Seq Workflow for Read Quantification, Differential Expression, and Pathway Enrichment Analysis
bioinformatics conda high-throughput reproducibility rna-seq singularity snakemake snakemake-workflow transcriptomics apptainer ideal renv genetonic pcaexplorer clusterprofiler deseq2 differential-expression salmon pathway-enrichment-analysis quality-control
Language:R 18