redst4r

cNMF

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

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

pybustools

Python functions to read the kallisto-bustools format

pyDiffusionMaps

Diffusion maps for python

pyHematoFatePrediction

Python code to [Buggenthin2017]

riemannian_latent_space

Riemannian metrics to measure distances in latent space of VAEs

rnaseqtools

Python code for handling various aspects of RNAseq data

sctools

Tools that come handy when working in scanpy all day long

stacked_denoising_autoencoders

trying to redo the Vincent2010 paper

redst4r/sctools

Tools that come handy when working in scanpy all day long

redst4r/rnaseqtools

Python code for handling various aspects of RNAseq data

redst4r/cNMF

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

redst4r/pybustools

Python functions to read the kallisto-bustools format

redst4r/anndata2ri

Convert between AnnData and SingleCellExperiment

redst4r/birthdeathpy

Discrete Self Replicating Birth Death Process

redst4r/bustools_cli-rs

Bustools CLI implementation in Rust

redst4r/cellBrowser

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

redst4r/cellbrowser_automation

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

redst4r/CellphoneDB

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

redst4r/cnvpy

python version of inferCNV

redst4r/crukiopy_release

Code for the STORMing Cancer Esophagus Atlas paper

redst4r/fastfibonacci-rs

Fast fibonacci coding/compression of integers

redst4r/gssnng

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

redst4r/infercnvpy

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

redst4r/liana-py

LIANA+: an all-in-one framework for cell-cell communication

redst4r/newpfd-rs

NewPFD compression/decompression of integers in Rust

redst4r/nvim_config

redst4r/otclustpy

Python package to assess cluster stability using Optimal transport, inspired by the `OTclust` R-package.

redst4r/phantompy

Python analog of the PhantomPurgeR algorithm to remove index-swapped reads in RNAseq

redst4r/pynndescent

A Python nearest neighbor descent for approximate nearest neighbors

redst4r/pytidyverse

Convenience for importing standard packages

redst4r/rust_shadow

rnaseq error estimation in rust

redst4r/rustbustools

Kallisto bustools in Rust

redst4r/rustphantompurger

Rust implementation of PhantomPurger

redst4r/scCODA

A statistical test for compositional changes in scRNA

redst4r/scHCLpy

A simplistic python version of the scHCL R package

redst4r/storming3

redst4r/storming_page

redst4r/unseenspecies

Unseen species estimators