differential-expression
There are 206 repositories under differential-expression topic.
owkin/PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
dmcable/spacexr
Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
theislab/diffxpy
Differential expression analysis for single-cell RNA-seq data.
tidyomics/tidybulk
Brings bulk and pseudobulk transcriptomics to the tidyverse
saeyslab/multinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
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.
nf-core/differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
nunofonseca/irap
integrated RNA-seq Analysis Pipeline
jackbibby1/SCPA
R package for pathway analysis in scRNA-seq data
snakemake-workflows/rna-seq-kallisto-sleuth
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
wckdouglas/diffexpr
Porting DESeq2 into python via rpy2
Russel88/DAtest
Compare different differential abundance and expression methods
BaderLab/scClustViz
Explore and share your scRNAseq clustering results
heiniglab/scPower
Experimental design framework for scRNAseq population studies (eQTL and DE)
grimmlab/BookChapter-RNA-Seq-Analyses
Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq analysis
KatrionaGoldmann/volcano3D
An R package to plot interactive three-way differential expression analysis
mritchielab/GlimmaV2
interactive plots for differential expression analysis
nf-core/lncpipe
UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
noamteyssier/adpbulk
pseudobulking on an AnnData object
federicomarini/ideal
Interactive Differential Expression AnaLysis - DE made accessible and reproducible
himelmallick/Tweedieverse
Differential analysis of multi-omics data based on the Tweedie distribution
theislab/batchglm
Fit generalized linear models in python.
DeplanckeLab/ASAP
ASAP : Automated Single-cell Analysis Pipeline
lpantano/DEGreport
Create a cromphensive report of DEG list coming from any analysis of RNAseq data
stemangiola/bioc_2020_tidytranscriptomics
Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap
refinery-platform/heatmap-scatter-dash
Interactive visualizations for differential expression
Bohdan-Khomtchouk/Microscope
ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps
olgatsiouri1996/biomisc_R
command line bioinformatic scripts written in R
shao-lab/MAnorm
A robust model for quantitative comparison of ChIP-Seq data sets.
hemberg-lab/D3E
Discrete Distributional Differential Expression
allielarocco/Microarray-Analysis
Microarray Analysis Pipeline in Python
btmonier/vidger
Make rapid visualizations of RNA-seq data in R
fperraudeau/singlecellworkflow
Tutorial for the analysis of scRNA-seq data in R
lingfeiwang/normalisr
Causal inference, differential expression, and co-expression for scRNA-seq
sanjaynagi/rna-seq-pop
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
tucca-cellag/tucca-rna-seq
TUCCA's RNA-Seq Workflow for Read Quantification, Differential Expression, and Pathway Enrichment Analysis