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anndata2ri

Convert between AnnData and SingleCellExperiment

anndata_oom

AnnData OOM tools

anon

tweet about anonymous Wikipedia edits from particular IP address ranges

arboreto

A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.

bioconda-recipes

Conda recipes for the bioconda channel.

birthdeathpy

Discrete Self Replicating Birth Death Process

bustools_cli-rs

Bustools CLI implementation in Rust

cellbrowser

Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org

cellbrowser_automation

Run cellbrowser on multiple datasets, creating a hierachy from a simple .yaml

cellphonedb

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

cnmf

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

cnvpy

python version of inferCNV

crukiopy_release

Code for the STORMing Cancer Esophagus Atlas paper

fastfibonacci-rs

Fast fibonacci coding/compression of integers

gssnng

Gene Set Scoring on the Nearest Neighbor Graph (gssnng) for Single Cell RNA-seq (scRNA-seq) using AnnData h5ad files.

gsva

A command-line interface and python module for R's GSVA bioconductor package

hematofateprediction

Code accompanying "Prospective identification of hematopoietic lineage choice by deep learning", Nature methods, in revision

infercnv

Inferring CNV from Single-Cell RNA-Seq

infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

lasagnetrainer

training neural networks implemented with lasagne

mnist_toydata

some code to compose MNIST digits into more complex images/arangements

movietools

python code to deal with time-lapse microscopy data

ms_plotting

newpfd-rs

NewPFD compression/decompression of integers in Rust

nf-10x-kallisto

kallisto quantification of a cellranger-processed 10x experiment (its bamfile)

nf-10x-pathseq

Nextflow pipeline for pathogen discovery via gatk-pathseq on scRNAseq

nvim_config

panama-papers-dataset-2016

Structured data about Panama papers collected from official ICIJ website

paperlda

LDA on research papers in my bibliography

particlefilter

Particle filtering inference for stochastic dynamical systems