Dana Pe'er Lab

Computational Biology @ Memorial Sloan Kettering Cancer Center

New York, NY

Pinned Repositories

cellrank
CellRank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data.
1 2 01
ENVI
Language:Python34 3 133
Harmony
Harmony framework for connecting scRNA-seq data from discrete time points
Language:Jupyter Notebook44 8 2012
magic
MAGIC - imputation and de-noising single-cell RNA seq data sets
Language:Jupyter Notebook21 3 012
Palantir
Single cell trajectory detection
Language:Jupyter Notebook203 10 11745
PhenoGraph
Subpopulation detection in high-dimensional single-cell data
Language:Python59 6 1425
scKINETICS
Code for scKINETICS (ISMB 2023)
Language:Jupyter Notebook20 2 43
SEACells
SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
Language:Jupyter Notebook140 7 5526
seqc
Single-Cell Sequencing Quality Control and Processing Software
Language:Python16 3 76
spectra
Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
Language:Python131 6 2916

Dana Pe'er Lab's Repositories

dpeerlab/Palantir
Single cell trajectory detection
Language:Jupyter Notebook203 10 11745
dpeerlab/SEACells
SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
Language:Jupyter Notebook140 7 5526
dpeerlab/spectra
Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
Language:Python131 6 2916
dpeerlab/Harmony
Harmony framework for connecting scRNA-seq data from discrete time points
Language:Jupyter Notebook44 8 2012
dpeerlab/ENVI
Language:Python34 3 133
dpeerlab/scKINETICS
Code for scKINETICS (ISMB 2023)
Language:Jupyter Notebook20 2 43
dpeerlab/pdac-progression
Language:Jupyter Notebook9 2 13
dpeerlab/WassersteinWormhole
Transformer Based Embeddings of Wasserstein Distance
Language:Python9 3 00
dpeerlab/Lineage_Plasticity_in_CRPC
Language:Jupyter Notebook7 3 03
dpeerlab/SCLC_atlas-HTAN
Single-cell atlas of SCLC leveraging scRNA-seq, MIBI, and Vectra imaging, as part of the Human Tumor Atlas Network
Language:Jupyter Notebook7 3 36
dpeerlab/SpectraReproducibility
Notebooks for reproducing figures in the Spectra paper
Language:Jupyter Notebook5 4 32
dpeerlab/ArchR
ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
Language:R4 0 04
dpeerlab/SpaceFold
Language:HTML4 4 11
dpeerlab/SpaceFold_paper
The repository contains scripts used in the manuscript.
Language:Jupyter Notebook4 4 0
dpeerlab/SEACellsReproducibility
Notebooks for reproducing figures in the SEACells manuscript
Language:Jupyter Notebook2 2 0
dpeerlab/Treg_depletion_reproducibility
Code related to analyses in Glasner, Rose, Sharma, et al Nature Immunology 2023.
Language:HTML2 4 00
dpeerlab/cytopus
Single cell omics biology annotations
Language:Jupyter Notebook1 0 0
dpeerlab/MERlin
MERFISH decoding software
Language:Python1 1 50
dpeerlab/mssi
Language:Jupyter Notebook10
dpeerlab/benchkit
Scripts for managing and processing large number of samples, also providing a CLI.
2 0
dpeerlab/cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
Language:Jupyter Notebook0 0
dpeerlab/docker-cellranger
Dockerized Cell Ranger
Language:Shell0 0
dpeerlab/docker-cellranger-arc
Dockerized Cell Ranger ARC
Language:Shell0 0
dpeerlab/ecosystem-packages
Register pe'er lab packages to scverse ecosystem
Language:Python
dpeerlab/PrismSpot
Language:Jupyter Notebook3 0
dpeerlab/scing
SCING: Single-Cell pIpeliNe Garden (pronounced as "sing" /siŋ/)
Language:Python0 01
dpeerlab/sharp
A single-cell demultiplexing pipeline, the sharp (♯)
Language:Jupyter Notebook0 0
dpeerlab/STAR
RNA-seq aligner
Language:C++
dpeerlab/wdl-cellranger-arc
WDLized Cell Ranger ARC
Language:WDL0 0
dpeerlab/wdl-cellranger-gex
WDLized Cell Ranger GEX
Language:WDL0 0