iandriver

scicast

Single Cell Iterative Clustering and Significance Testing

RNA-sequence-tools

Tools for RNA seq and gene annotation

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

affy_reader

Python scripts for parsing affymetrix array cel and cdf files

Bioinformatics

Random Bioinformatics

python_class

files for UCSF Cell Hackers Class

gene_graphlasso

Creates network graphs from single cell expression data.

sra_fetch

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

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

GEOparse

Python library to access Gene Expression Omnibus Database (GEO)

HASSL_Homogeneous_Analysis_of_SRA_rnaSequencing_Libraries

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_practice

Random

RCA

R package for robust clustering of single cell RNA sequencing data

Rnaseq

Rnaseq pipeline deliverable

scanpy

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

seaborn

Statistical data visualization using matplotlib

signac

R toolkit for the analysis of single-cell chromatin data

wishbone

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

ZIFA

Zero-inflated dimensionality reduction algorithm for single-cell data