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differential-expression

Here are 134 public repositories matching this topic...

theislab / diffxpy

Differential expression analysis for single-cell RNA-seq data.

bioinformatics tensorflow transcriptomics gene-set-enrichment differential-expression single-cell-rna-seq

Updated Oct 11, 2022
Python

dmcable / spacexr

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

differential-expression spatial-transcriptomics cell-type-identification

Updated Oct 31, 2022
HTML

tidybulk

stemangiola / tidybulk

Brings bulk and pseudobulk transcriptomics to the tidyverse

Updated Sep 28, 2022
R

nunofonseca / irap

integrated RNA-seq Analysis Pipeline

rna-seq pipeline gene-expression rna-seq-analysis differential-expression transcript-quantification single-cell-rna-seq irap bulk-rna-seq exon-quantification

Updated Feb 6, 2019
R

wckdouglas / diffexpr

Porting DESeq2 and DEXSeq into python via rpy2

python rna-seq differential-expression

Updated Apr 16, 2022
Jupyter Notebook

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.

Updated Oct 27, 2022
Python

snakemake-workflows / rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

rna-seq snakemake reproducibility kallisto differential-expression sleuth sciworkflows

Updated Oct 30, 2022
R

BaderLab / scClustViz

Explore and share your scRNAseq clustering results

r ui shiny scrna-seq single-cell differential-expression clustering-evaluation scrnaseq scrna-seq-analysis

Updated Aug 3, 2022
R

Russel88 / DAtest

Compare different differential abundance and expression methods

metagenomics rnaseq auc proteomics metabolomics microbiome false-positive-control differential-expression 16s otu marker-gene-analysis relative-abundances compare-methods differential-abundance-methods

Updated Mar 8, 2022
R

heiniglab / scPower

Experimental design framework for scRNAseq population studies (eQTL and DE)

single-cell differential-expression eqtl power-analysis

Updated Oct 28, 2022
R

refinery-platform / heatmap-scatter-dash

Interactive visualizations for differential expression

visualization docker refinery differential-expression

Updated Jun 21, 2022
Python

federicomarini / ideal

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

rna-seq r shiny reproducible-research bioconductor user-friendly rna-seq-analysis differential-expression

Updated Oct 21, 2022
R

stemangiola / bioc_2020_tidytranscriptomics

Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap

r workshop heatmap tidy-data tidyverse pca bioconductor mds transcriptomics differential-expression tidybulk bioc2020

Updated Sep 23, 2020
R

Bohdan-Khomtchouk / Microscope

ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps

rna-seq heatmap computational-biology gene-expression statistical-analysis gene-ontology chip-seq network-analysis differential-expression principal-component-analysis r-programming

Updated Oct 12, 2017
R

nf-core / lncpipe

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

workflow pipeline nextflow rna transcriptome rna-seq-analysis differential-expression lncrna non-coding nf-core long-non-coding

Updated Oct 4, 2022
Nextflow

theislab / batchglm

Fit generalized linear models in python.

tensorflow differential-expression generalized-linear-models

Updated Oct 31, 2022
Python

grimmlab / BookChapter-RNA-Seq-Analyses

Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq analysis

bioinformatics pipeline differential-expression rnaseq-analysis

Updated May 17, 2021
Shell

volcano3D

KatrionaGoldmann / volcano3D

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

package cran bioinformatics rna-seq interactive plotly gene-expression omics transcriptomics differential-expression differential-expression-analysis volcanoplots

Updated Sep 26, 2022
R

olgatsiouri1996 / biomisc_R

command line bioinformatic scripts written in R

bioinformatics r statistics fasta differential-expression

Updated Jun 5, 2022
R

btmonier / vidger

Make rapid visualizations of RNA-seq data in R

visualization r gene-expression rna-seq-analysis differential-expression data-munging

Updated Jul 15, 2019
R

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