Pinned Repositories
cellrank
CellRank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data.
ENVI
Harmony
Harmony framework for connecting scRNA-seq data from discrete time points
magic
MAGIC - imputation and de-noising single-cell RNA seq data sets
Palantir
Single cell trajectory detection
PhenoGraph
Subpopulation detection in high-dimensional single-cell data
scKINETICS
Code for scKINETICS (ISMB 2023)
SEACells
SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
seqc
Single-Cell Sequencing Quality Control and Processing Software
spectra
Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
Dana Pe'er Lab's Repositories
dpeerlab/PhenoGraph
Subpopulation detection in high-dimensional single-cell data
dpeerlab/magic
MAGIC - imputation and de-noising single-cell RNA seq data sets
dpeerlab/wishbone
Wishbone is an algorithm to align cells along developmental trajectories with branches
dpeerlab/lung-development-cancer-progression
Single cell analysis in regenerative lineages and immune-mediated pruning in lung cancer metastasis
dpeerlab/seqc
Single-Cell Sequencing Quality Control and Processing Software
dpeerlab/Symphony
Symphony algorithm for inference of cell type specific gene regulatory networks from scRNA-seq and ATAC-seq
dpeerlab/Vectra_Imaging_pipeline
Vectra Imaging Quality Control and Processing Pipeline
dpeerlab/dli_gpr
GP regression model for DLI therapy data for CML
dpeerlab/pdac-tumorigenesis-scATAC
Analysis of scATAC-seq data from early pancreatic cancer initiation.
dpeerlab/cellrank-deprecated
Mapping the fate of single cells using RNA Velocity
dpeerlab/cyt3
Matlab GUI for analysis of mass cytometry data
dpeerlab/DoubletDetection
Doublet detection in single-cell RNA-seq data.
dpeerlab/DREMI
dpeerlab/BISCUIT_SingleCell_IMM_ICML_2016
R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells.
dpeerlab/cellrank
CellRank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data.
dpeerlab/CONEXIC
COpy Number and EXpression In Cancer (CONEXIC)
dpeerlab/CTLA4KO
dpeerlab/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
dpeerlab/scanpy
Single-Cell Analysis in Python. Scales to >1M cells.
dpeerlab/tides
dpeerlab/velocyto_mapping
dpeerlab/cellranger
10x Genomics Single Cell 3' Gene Expression and VDJ Assembly
dpeerlab/h5
Simple wrapper around pandas hdf5 method to allow safe usage
dpeerlab/MAGIC_EMT
dpeerlab/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.
dpeerlab/mnnpy
An implementation of MNN (Mutual Nearest Neighbors) correct in python.
dpeerlab/msk-scri
dpeerlab/sctools
Utilities for large scale distributed single cell data processing
dpeerlab/wdl-cellranger-beam
WDLized Cell Ranger Cell Plex
dpeerlab/wdl-transgenes
Creating a genome index for the STAR aligner with transgenes