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cardinalscripts

cardinalworkflows

Datasets and workflows for Cardinal mass spectrometry imaging package

cellgrid

Cell classification by learning known phenotypes

chip-seq-analysis

ChIP-seq analysis notes from Ming Tang

deeptools

Tools to process and analyze deep sequencing data.

epigenomeanalysistutorial-2020

This website contains material for an epigenome analysis tutorial that covers ATAC-seq analysis and integration with TF motifs and gene expression

fit-sne

Fast Fourier Transform-accelerated Interpolation-based t-SNE (FIt-SNE)

galapagos-examples

Galapagos scRNA-Seq clustering examples

gatk-tools

Utilities for processing sequencing data and genomic variants using GATK

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics and data science

immunology_tools

ims_processing_evaluation

lecture_i2ml

gh-page

mofa

Multi-Omics Factor Analysis

msipl

Python Implementation of the msiPL by Abdelmoula et al.

ngs-pipe

NGS-pipe: next-generation sequencing pipelines for precision oncology

ofxtsne

t-SNE dimensionality reduction technique for openFrameworks

opentsne

Extensible, parallel implementations of t-SNE

pancreatic-endocrinogenesis

This repository contains all scripts to reproduce the results from:

panoply

Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)

pyflow-atacseq

ATAC-seq snakemake pipeline

regnet

regNet is an R package that utilizes gene expression and copy number data to learn regulatory networks for the quantification of potential impacts of individual gene expression alterations on user-defined target genes via network propagation.

rna-seq-analysis

RNAseq analysis notes from Ming Tang

rna-seq-tsne

The art of using t-SNE for single-cell transcriptomics

sc-rna-seq-pipeline

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

scanpy-tutorials

Scanpy Tutorials.

scrnaseq-analysis-notes

scRNAseq analysis notes from Ming Tang

seurat

R toolkit for single cell genomics

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"