Pirasteh's repositories
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
getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
lecture_i2ml
gh-page
MOFA
Multi-Omics Factor Analysis
msiPL
Python Implementation of the msiPL by Abdelmoula et al.
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
RNA-seq-analysis
RNAseq analysis notes from Ming Tang
rna-seq-tsne
The art of using t-SNE for single-cell transcriptomics
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"
Single-Molecule-Imaging-of-Transcription-Dynamics-in-Somatic-Stem-Cells
Data matrices and scripts needed for running analyses in Wheat et al, Nature 2020
springer_free_books
Python script to download all Springer books released for free during the 2020 COVID-19 quarantine
variational-autoencoder
Variational autoencoder implemented in tensorflow and pytorch (including inverse autoregressive flow)
voronoi_treemap_rJava
Voronoi Treemaps in R using ArlindNocaj/Voronoi-Treemap-Library