135 skills found · Page 1 of 5
griffithlab / Rnaseq TutorialInformatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
statOmics / TradeSeqTRAjectory-based Differential Expression analysis for SEQuencing data
theislab / DiffxpyDifferential expression analysis for single-cell RNA-seq data.
interactivereport / Cellxgene VIPEnables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
alyssafrazee / BallgownBioconductor package "ballgown", devel version. Isoform-level differential expression analysis in R.
iDEP-SDSU / IdepIntegrated Differential Expression and Pathway analysis
erilu / Bulk Rnaseq AnalysisA complete guide for analyzing bulk RNA-seq data. Go from raw FASTQ files to mapping reads using STAR and differential gene expression analysis using DESeq2, using example data from Guo et al. 2019.
nanoporetech / Pipeline Transcriptome DePipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
snakemake-workflows / Single Cell Rna SeqA single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
bvieth / PowsimRPower analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
r-bioinformatics / EdgePyA Python implementation of edgeR for differential expression analysis
thelovelab / RnaseqGeneRNA-seq workflow: exploratory analysis and differential expression
snakemake-workflows / Rna Seq Kallisto SleuthA Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
wyguo / ThreeDRNAseqA pipeline for differential expression and differential alternative splicing analysis
epigen / Dea LimmaA Snakemake workflow and MrBiomics module for performing and visualizing differential analyses of NGS data powered by the R package limma.
nf-core / CircrnacircRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
olgabot / Rna Seq Diff ExprnRNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).
epigen / Dea SeuratA Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
pachterlab / EdgePythonedgePython is a Python implementation of the Bioconductor edgeR package for differential analysis of genomics count data. It also includes a new single-cell differential expression method that extends the NEBULA-LN negative binomial mixed model with edgeR's TMM normalization and empirical Bayes dispersion shrinkage.
fgcz / ProlfquaDifferential Expression Analysis tool box R lang package for omics data
