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Palantir
Single cell trajectory detectionSEACells
SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics dataspectra
Supervised Pathway DEConvolution of InTerpretable Gene ProgRAmsHarmony
Harmony framework for connecting scRNA-seq data from discrete time pointsENVI
scKINETICS
Code for scKINETICS (ISMB 2023)lung-development-cancer-progression
Single cell analysis in regenerative lineages and immune-mediated pruning in lung cancer metastasisSymphony
Symphony algorithm for inference of cell type specific gene regulatory networks from scRNA-seq and ATAC-seqpdac-progression
MaskRCNN_cell
An implementation of Mask R-CNN designed for single-cell instance segmentation in the context of multiplexed tissue imagingLineage_Plasticity_in_CRPC
SCLC_atlas-HTAN
Single-cell atlas of SCLC leveraging scRNA-seq, MIBI, and Vectra imaging, as part of the Human Tumor Atlas NetworkWassersteinWormhole
Transformer Based Embeddings of Wasserstein DistanceSpectraReproducibility
Notebooks for reproducing figures in the Spectra paperVectra_Imaging_pipeline
Vectra Imaging Quality Control and Processing PipelineSpaceFold_paper
The repository contains scripts used in the manuscript.dli_gpr
GP regression model for DLI therapy data for CMLSpaceFold
Treg_depletion_reproducibility
Code related to analyses in Glasner, Rose, Sharma, et al Nature Immunology 2023.DREMI
cyt3
Matlab GUI for analysis of mass cytometry dataSEACellsReproducibility
Notebooks for reproducing figures in the SEACells manuscriptCTLA4KO
tides
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-ercellrank
CellRank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data.CONEXIC
COpy Number and EXpression In Cancer (CONEXIC)mssi
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