dpeerlab/scKINETICS

Stars
20
Rank 1,116,068 (Top 23 %)
Language
Jupyter Notebook
Created almost 2 years ago
Updated 11 months ago

dpeerlab/scKINETICS

dpeerlab

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Code for scKINETICS (ISMB 2023)

Palantir

Single cell trajectory detection

Jupyter Notebook

SEACells

SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data

Jupyter Notebook

spectra

Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms

Harmony

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

Jupyter Notebook

ENVI

lung-development-cancer-progression

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

Symphony

Symphony algorithm for inference of cell type specific gene regulatory networks from scRNA-seq and ATAC-seq

Jupyter Notebook

pdac-progression

Jupyter Notebook

MaskRCNN_cell

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

Jupyter Notebook

Lineage_Plasticity_in_CRPC

Jupyter Notebook

SCLC_atlas-HTAN

Single-cell atlas of SCLC leveraging scRNA-seq, MIBI, and Vectra imaging, as part of the Human Tumor Atlas Network

Jupyter Notebook

WassersteinWormhole

Transformer Based Embeddings of Wasserstein Distance

SpectraReproducibility

Notebooks for reproducing figures in the Spectra paper

Jupyter Notebook

Vectra_Imaging_pipeline

Vectra Imaging Quality Control and Processing Pipeline

Jupyter Notebook

SpaceFold_paper

The repository contains scripts used in the manuscript.

Jupyter Notebook

dli_gpr

GP regression model for DLI therapy data for CML

Jupyter Notebook

SpaceFold

pdac-tumorigenesis-scATAC

Analysis of scATAC-seq data from early pancreatic cancer initiation.

Jupyter Notebook

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 data

SEACellsReproducibility

Notebooks for reproducing figures in the SEACells manuscript

Jupyter Notebook

CTLA4KO

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-er

cellrank

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

Jupyter Notebook