dpeerlab

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:Python42 3 206
Harmony
Harmony framework for connecting scRNA-seq data from discrete time points
Language:Jupyter Notebook46 8 2112
magic
MAGIC - imputation and de-noising single-cell RNA seq data sets
Language:Jupyter Notebook26 3 012
Palantir
Single cell trajectory detection
Language:Jupyter Notebook233 11 12753
PhenoGraph
Subpopulation detection in high-dimensional single-cell data
Language:Python66 6 1425
scKINETICS
Code for scKINETICS (ISMB 2023)
Language:Jupyter Notebook21 2 43
SEACells
SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
Language:Jupyter Notebook153 6 6027
seqc
Single-Cell Sequencing Quality Control and Processing Software
Language:Python16 3 75
spectra
Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
Language:Python161 6 3218

dpeerlab's Repositories

dpeerlab/Palantir
Single cell trajectory detection
Language:Jupyter Notebook233 11 12753
dpeerlab/spectra
Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
Language:Python161 6 3218
dpeerlab/SEACells
SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
Language:Jupyter Notebook153 6 6027
dpeerlab/Harmony
Harmony framework for connecting scRNA-seq data from discrete time points
Language:Jupyter Notebook46 8 2112
dpeerlab/ENVI
Language:Python42 3 206
dpeerlab/scKINETICS
Code for scKINETICS (ISMB 2023)
Language:Jupyter Notebook21 2 43
dpeerlab/WassersteinWormhole
Transformer Based Embeddings of Wasserstein Distance
Language:Python13 4 11
dpeerlab/pdac-progression
Language:Jupyter Notebook10 2 14
dpeerlab/progressive-plasticity-crc-metastasis
Notebooks for generating figures in "Progressive Plasticity During Colorectal Cancer Metastasis"
Language:Jupyter Notebook102
dpeerlab/SpectraReproducibility
Notebooks for reproducing figures in the Spectra paper
Language:Jupyter Notebook7 4 33
dpeerlab/ArchR
ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
Language:R4 0 04
dpeerlab/mssi
Language:Jupyter Notebook3 2 10
dpeerlab/cytopus
Single cell omics biology annotations
Language:Jupyter Notebook2 0 0
dpeerlab/PrismSpot
Language:Jupyter Notebook2 3 0
dpeerlab/Treg_depletion_reproducibility
Code related to analyses in Glasner, Rose, Sharma, et al Nature Immunology 2023.
Language:HTML2 4 00
dpeerlab/Brain-metastasis-TME
Language:Jupyter Notebook1 2 0
dpeerlab/cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
Language:Jupyter Notebook1 1 0
dpeerlab/MERlin
MERFISH decoding software
Language:Python1 1 50
dpeerlab/MitoEJ-paper-analysis
Code for Figures for MitoEJ paper by Yi and Max
Language:Jupyter Notebook1 2 0
dpeerlab/STAR
RNA-seq aligner
Language:C++1 1 0
dpeerlab/benchkit
Scripts for managing and processing large number of samples, also providing a CLI.
2 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:Python0 0
dpeerlab/integrateCNV
Language:Jupyter Notebook
dpeerlab/scing
SCING: Single-Cell pIpeliNe Garden (pronounced as "sing" /siŋ/)
Language:Python0 01
dpeerlab/segger_dev
Language:Python0 0
dpeerlab/sharp
A single-cell demultiplexing pipeline, the sharp (♯)
Language:Jupyter Notebook0 5
dpeerlab/wdl-cellranger-arc
WDLized Cell Ranger ARC
Language:wdl0 0
dpeerlab/wdl-cellranger-gex
WDLized Cell Ranger GEX
Language:wdl0 0