a software package for analysis and exploration of single-cell RNA-seq datasets

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

Course on analysis of NGS data (RNA-Seq. and ATAC-Seq.) using Galaxy

NicheNet: predict active ligand-target links between interacting cells

A pixelclassification based multiplexed image segmentation pipeline

Use RMarkdown to generate PDF Conference Posters via HTML

Power 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 ev…

Tools to process and analyze deep sequencing data.

Code Repository for Satpathy Granja et al 2019

List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Template for project directory structure.

Midnight is a Jekyll theme for GitHub Pages

R toolkit for single cell genomics

ENCODE ATAC-seq pipeline

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

Lollipop-style mutation diagrams for annotating genetic variations.

Toolkit for processing sequences in FASTA/Q formats

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

MACS -- Model-based Analysis of ChIP-Seq

Materials presented at the BiocNYC meet-up

R package with motifs for use with chromVAR

Quick mining and visualization of NGS data by integrating genomic databases

mdlabbook is a markdown-format lab notebook