A repository to store the existing pipelines to process the various CoLabs datasets

Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data

inference of transcription factor activity at the single cell level

RF model and functions to estimate tumor purity using methylation data

Method for calculating tumor purity and adjusting Illumina 450/850K DNA methylation beta values.

🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips

scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.

R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients

R package for DNA methylation analysis

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing and spatial data in an easy and efficient way.

A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessible.

scATAC-seq data analysis tools and papers

High dimensional weighted gene co-expression network analysis

scWGCNA

Reference mapping for single-cell genomics

Provides functionality for analyzing RT-qPCR and ChIP-qPCR data and generating plots of results

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

A list of scRNA-seq analysis tools

Machine learning and deep learning resources

Classical equations and diagrams in machine learning

Information Theory and Distance Quantification with R

EMBL-EBI single cell RNA-seq analysis in R course practicals

BioC2021: Where Software and Biology Connect

Short lessons from FAS Informatics coffee hour

Identify and correct invalid gene symbols

List of Consultants/Companies that provide bioinformatic solutions / services