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Search results for python single cell rna seq

single-cell-rna-seq x

36 search results found

Squidpy ⭐ 362

Spatial Single Cell Analysis in Python

DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis

Cellrank ⭐ 279

CellRank: dynamics from multi-view single-cell data

Diffxpy ⭐ 157

Differential expression analysis for single-cell RNA-seq data.

Kb_python ⭐ 132

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

Liana Py ⭐ 99

LIANA+: an all-in-one framework for cell-cell communication

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Cell_blast ⭐ 74

A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.

Cassiopeia ⭐ 67

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

Single-Cell Clustering Assessment Framework

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

Pipeliner ⭐ 44

An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.

Cell2cell ⭐ 44

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics

Deep Learning based cell composition analysis with Scaden.

Pyrovelocity ⭐ 31

𝒫robabilistic modeling of RNA velocity ⬱

scDCC: Single Cell Deep Constrained Clustering

Split Seq_demultiplexing ⭐ 25

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

Stackeddae ⭐ 20

Stacked Denoising AutoEncoder based on TensorFlow

Sctcrseq ⭐ 18

Processing of single cell RNAseq data for the recovery of TCRs in python

Detection of allele-specific subclonal copy number variations from single-cell transcriptomic data.

Single Cell Multi-omics deep clustering

Mitochondrial Alteration Enrichment and Genome Analysis Toolkit

Discrete Distributional Differential Expression

tGPLVM: A Nonparametric, Generative Model for Manifold Learning with scRNA-seq experimental data

Toolchest Client Python ⭐ 13

Toolchest Python client

Divisive Intelligent K-Means algorithm (DiviK) for joint feature selection and clustering of heavily multidimensional data.

Deep exponential families for single-cell data.

Transmorph ⭐ 10

Computational framework for dataset integration

Discovering de novo shared transcriptional programs in single cancer cells

Python package with CLI for downstream analysis of single cell methylation data.

Pigx_scrnaseq ⭐ 9

Pipeline for analysis of Dropseq single cell data

Simulation based inference of differentiation trajectories from RNA velocity fields.

A tool to quantify transposable elements expression in scRNA-seq

MuDCoD: Multi-subject Dynamic Community Detection

Generate the UMI count matrix from CEL-Seq2 sequencing data

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