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archr

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

biscuit_singlecell_imm_icml_2016

R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells.

cellranger

10x Genomics Single Cell 3' Gene Expression and VDJ Assembly

cellrank

CellRank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data.

cellrank-deprecated

Mapping the fate of single cells using RNA Velocity

conexic

COpy Number and EXpression In Cancer (CONEXIC)

ctla4ko

cyt3

Matlab GUI for analysis of mass cytometry data

cytopus

Single cell omics biology annotations

dli_gpr

GP regression model for DLI therapy data for CML

docker-cellranger

Dockerized Cell Ranger

docker-cellranger-arc

Dockerized Cell Ranger ARC

doubletdetection

Doublet detection in single-cell RNA-seq data.

dpeerlab-website

A copy of old lab website from Columbia (https://dpeerlab.github.io/dpeerlab-website/index.html). Content is not updated since 2017. New website: https://www.mskcc.org/research-areas/labs/dana-pe-er

dremi

ecosystem-packages

Register pe'er lab packages to scverse ecosystem

envi

h5

Simple wrapper around pandas hdf5 method to allow safe usage

harmony

Harmony framework for connecting scRNA-seq data from discrete time points

lineage_plasticity_in_crpc

lung-development-cancer-progression

Single cell analysis in regenerative lineages and immune-mediated pruning in lung cancer metastasis

magic

MAGIC - imputation and de-noising single-cell RNA seq data sets

magic_emt

maskrcnn_cell

An implementation of Mask R-CNN designed for single-cell instance segmentation in the context of multiplexed tissue imaging

merlin

MERFISH decoding software

mibi_pre-processing_pipeline

This repo is for MIBI data preprocessing and is the Python 3 version implementation of its original MATLAB version (https://github.com/lkeren/MIBIAnalysis) from Keren et al Cell 2018.

mnnpy

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

msk-scri

mssi

palantir

Single cell trajectory detection