johnmous

EmbryoTimecourse2018

Data and analysis scripts for our Embryo Timecourse paper.

singlecelldb

An actionable database of publicly available single-cell RNA-seq data

SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

CellReports_2018_heart_scRNAseq

data for study of gene expression of non-myocytes in the heart, Skelly et al. 2018 Cell Reports http://dx.doi.org/10.1016/j.celrep.2017.12.072

interactive_plotting

HECA

Human embryonic cell altas

gffutils

GFF and GTF file manipulation and interconversion

X-Reactivation

Analysis scripts for the Vertesy 2018 paper: "Parental haplotype specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells"

scanpy

Single-cell analysis in Python. Scales to >1M cells.

velocyto.R

RNA velocity estimation in R

velocyto.py

RNA velocity estimation in Python

STAR

RNA-seq aligner

BUS_notebooks_python

bioconda-recipes

Conda recipes for the bioconda channel.

Palantir

Single cell trajectory detection

avocado

Avocado is a multi-scale deep tensor factorization model that learns a latent representation of the human epigenome and enables imputation of epigenomic experiments that have not yet been performed.

graph2gauss

Gaussian node embeddings. Implementation of "Deep Gaussian Embedding of Graphs: Unsupervised Inductive Learning via Ranking".

collect-columns

RNAseq_multi_method

dca

Deep count autoencoder for denoising scRNA-seq data

batchelor

Clone of the Bioconductor repository for the batchelor package.

pytest-workflow

Configure workflow/pipeline tests using yaml files.

wdl

Workflow Description Language - Specification and Implementations

dyno

Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

crosstalk

Inter-htmlwidget communication for R (with and without Shiny)

StemID

Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data.

seurat

R toolkit for single cell genomics

biscuit

BISulfite-seq CUI Toolkit