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Starred repositories

29 stars written in R
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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…

R 1,419 618 Updated May 31, 2023

📊 A universal enrichment tool for interpreting omics data

R 1,185 265 Updated Mar 22, 2026

Publication-ready volcano plots with enhanced colouring and labeling

R 457 86 Updated Dec 3, 2025

A repository for setting up a RNAseq workflow

R 455 179 Updated Apr 10, 2017

Fast Gene Set Enrichment Analysis

R 434 71 Updated Jan 2, 2026

An R package for downstream data analysis of microbiome omics data

R 273 77 Updated Mar 22, 2026

Create Standalone Installable Shiny Apps

R 267 35 Updated Aug 28, 2025

Visualization of Functional Enrichment Result

R 257 75 Updated Mar 26, 2026

Quality control for MinION sequencing data

R 217 43 Updated Mar 17, 2026

R package for microbiome biomarker discovery

R 194 41 Updated Feb 19, 2025

Transcript quantification import for modular pipelines

R 142 36 Updated Sep 30, 2025

Make Interactive Complex Heatmaps

R 139 26 Updated Jan 30, 2026

Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2

R 77 10 Updated Aug 30, 2016

Tools for visualising microbial community amplicon data

R 72 28 Updated Nov 3, 2025

Locate antiviral defence systems in prokaryotic genomes

R 70 13 Updated Oct 22, 2024

Create KEGG.db Package

R 64 19 Updated Jan 29, 2026

Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)

R 63 14 Updated Apr 12, 2021

Differential Count Data Analysis Toolbox

R 61 30 Updated Feb 5, 2024

Normalization for single cell RNA-seq data

R 51 11 Updated Jun 11, 2025

Various functions for analysis of microbial community data

R 47 12 Updated Oct 1, 2025

Create QC and summary reports for Alevin output

R 31 6 Updated Jan 27, 2026

An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis

R 28 9 Updated Jan 27, 2021
R 23 4 Updated Nov 9, 2025

A web-based application to perform Gene Set Enrichment Analysis (GSEA) using clusterProfiler and shiny R libraries

R 16 9 Updated Jan 27, 2020

An R package for automatically aggregating and summarizing lncRNA analysis results.

R 16 5 Updated Mar 5, 2019

Trinotate annotation report summaries in R

R 13 6 Updated Feb 24, 2016
R 7 8 Updated Jan 12, 2021