Stars
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Tools for correcting single cell barcodes for various scATAC-seq techniques and creating fragment files and spltting BAM files per cluster.
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
List of software packages for multi-omics analysis
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene reg…
SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
This is where TOG houses all of its workshop scripts, as well as details on its upcoming workshops and seminars.
This resource provides the code developed in the study of Jerby-Arnon _et al. "Single-cell RNA-seq of melanoma ecosystems reveals sources of T cell exclusion linked to immunotherapy clinical outcom…
The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This algorithm also works in bulk expression profiling data.)
ENCODE Uniform processing pipeline for ChIP-seq
Converts MySQL dump to SQLite3 compatible dump
chromatin Variability Across Regions (of the genome!)
ChIP-seq analysis notes from Ming Tang
🐛 How to use CENTIPEDE to determine if a transcription factor is bound.
ATAC-seq and DNase-seq processing pipeline
One of the 'BEST' markdown preview extensions for Atom editor!
R package for reading in & working with NucleoATAC outputs
Area proportional Venn and Euler diagrams in JavaScript