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affy_reader

Python scripts for parsing affymetrix array cel and cdf files

bioinformatics

Random Bioinformatics

clone-gut-model

model of drosophila intestine

empty_nn

Learning empty droplets in scRNAseq

falco

A quick and flexible single-cell RNA-seq processing framework on the cloud

gene_graphlasso

Creates network graphs from single cell expression data.

geoparse

Python library to access Gene Expression Omnibus Database (GEO)

hassl_homogeneous_analysis_of_sra_rnasequencing_libraries

ips17-bu3-single-cell

The full data and code for the paper: Prospective isolation and single cell profiling of NKX2-1+/CD47+ human lung progenitors derived from pluripotent stem cells. Hawkins et al. JCI

isee

R/shiny interface for interactive visualization of data in objects derived from the SummarizedExperiment class

magic

monocle-release

pyensembl

Python interface to ensembl reference genome metadata (exons, transcripts, etc...)

python_class

files for UCSF Cell Hackers Class

python_practice

random

rca

R package for robust clustering of single cell RNA sequencing data

rna-sequence-tools

Tools for RNA seq and gene annotation

rnaseq

Rnaseq pipeline deliverable

scanpy

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

scicast

Single Cell Iterative Clustering and Significance Testing

seaborn

Statistical data visualization using matplotlib

signac

R toolkit for the analysis of single-cell chromatin data

sra_fetch

GUI app for downloading whole SRA series or individual and metadata. Additional options for uploading to S3

wishbone

Wishbone is an algorithm to align cells along developmental trajectories with branches

zifa

Zero-inflated dimensionality reduction algorithm for single-cell data