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Starred repositories
resources for learning bioinformatics
A curated list of resources for learning bioinformatics.
Nextflow-orchestrated distributed data pipeline for processing and analyzing raw scRNA-seq files
A single-cell RNAseq pipeline for 10X genomics data
A simple RNA-Seq differential gene expression pipeline using Nextflow
A Nextflow implementation of the Tuxedo Suite of Tools: HISAT, StringTie & Ballgown
A DIY guide to gene ontology, pathway, and gene set enrichment analysis
Template for writing an Oxford University thesis in R Markdown; uses the OxThesis LaTeX template and was inspired by thesisdown.
This repository contains R workflows designed to calculate and visualize term enrichment for lists of genes
Working Demo on GO Enrichment Analysis using topGO, clusterProfiler and Enrichr/enrichR. Visit repo website for HTML output
Informatics 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 form…
A collection of utility scripts, data analysis pipeline, and documentation for RNA-Seq with non-model organisms
more extensive sample data for exploring various Trinity supported analysis modules
scrape REVIGO Gene Ontology web app and plot results
How to perform GO term enrichment analysis using topGO (Alexa et al., 2006).
DeepGenePredictor: A deep learning model for predicting gene expression levels with PyTorch, featuring linear regression and K-Fold cross-validation for robust performance evaluation.
A shiny application to perform differential gene expression analysis of count data using DESeq2. The app also allows unsupervised exploration of data using PCA and hierarchical clustering.
DESeq2Shiny2 is an R shiny application to handle NGS count data and perform unsupervised clustering and Differential Gene Expression Analysis using DESeq2.