Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

Workshop • Analysis of RNA-seq data

Interactive R package to quantify, analyse and visualise alternative splicing

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

ASAP : Automated Single-cell Analysis Pipeline

Gene-level general linear mixed model

Script to automate differential expression analysis using DESeq2, edgeR or limma-voom

📊 An R package of RNA-seq workflow

single cell and bulk RNASeq analysis scripts

An application for exploring and visualizing differential gene expression data created with DESeq2

Scripts to run differential expression analysis using DESeq2 package

Code and figures for the Differential Causal Inference (DCI) algorithm

Curare - A customizable and reproducible analysis pipeline for RNA-Seq experiments

Python framework for explainable omics analysis

Accurate, easy and integrated suit to compare RNA samples with different degradation levels, quantify decay rates per-transcript and correct for degradation-induced artifacts in differential gene/transcript comparisons

:tangerine: View the gene expression response to TNF and IL-17A with vanilla Javascript and HTML.

Comparison of gene usage in immune repertoires under different biological conditions

RNAseq workflow run using BASH, Nextflow, and Snakemake on AWS and GCP, developed as part of the NIH NIGMS Sandbox

RNA-seq alignment and analysis pipeline

Viper is a Snakemake workflow, aimed at performing the RNA-seq workflow of the paper 'Causes and consequences of a glutamine induced normoxic HIF1 activity for the tumor metabolism', Kappler et al. (2019) in a reproducible and automated manner

Worked with fellow peers at University of Pittsburgh under supervision of Dr. Junshu Bao, Department of Statistics, University of Pittsburgh, to do a Differential Gene Expression Analysis on a Dexamethasone treatment data set and incorporated Machine Learning into project.

bioTEA - A user friendly tool to perform transcript expression analysis

These are tutorials on a subset of tools available for processing raw RNAseq data. This if for HISAT2_SAMtools_Stringtie_gffcompare_ballgown pipeline or HISAT2_SAMtools_Stringtie_PrepDEanalysis.py_DESeq2 pipeline

An integrative resource for deubiquitinating enzymes (DUBs) served at https://labsyspharm.github.io/dubportal

Individual cell-based differential transcriptomic analysis across conditions

The package RNAseqAnalysis does the complete analysis of RNA seq data starting from raw reads. It provides the user with differnt functions like generation of qc report, filtering, assembly and GO-term annotation, differential expression analysis and heatmap generation, and Alternative splicing-site prediction

Temporal Integrative Genomics Analysis in R

Cellular​ ​signatures​ characterisation ​after​ ​carcinogenic​ ​chemical​ ​exposure​ ​in​ ​mammalian​ ​tissue.

Bayesian Gene Selection Criterion (BGSC) approach

Analysis of single and comparative transcriptomes