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Search results for python scrna seq

31 search results found

Dynamo Release ⭐ 383

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

Single cell perturbation prediction

Celltypist ⭐ 202

A tool for semi-automatic cell type classification

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

Souporcell ⭐ 134

Clustering scRNAseq by genotypes

Kb_python ⭐ 132

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

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.

Scperturb ⭐ 56

scPerturb: A resource and a python/R tool for single-cell perturbation data

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.

Cell2cell ⭐ 44

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

Cellhint ⭐ 44

A tool for semi-automatic cell type harmonization and integration

Cellxgene Gateway ⭐ 40

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.

a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.

Interactive software tool for the assignment of cell types in single-cell studies.

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

A tool for fast and accurate summarizing of variant calling format (VCF) files

Split Seq_demultiplexing ⭐ 25

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

Pathogentrack ⭐ 22

A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.

Cell2sentence Ft ⭐ 21

Cell2Sentence turns scRNA-seq data into text for LLM training.

Symphonypy ⭐ 19

Port of symphony algorithm of single-cell reference atlas mapping to Python

Demuxalot ⭐ 17

Reliable, scalable and demultiplexing for single-cell RNA sequencing. Improves genotypes with Expectation-Maximization

Visium Clustergrammer2 ⭐ 14

Spatial Transcriptomics Dashboard

Cell-type Assignment and Module Extraction based on a heterogeneous graph neural network.

Map single-cell transcriptomes to copy number evolutionary trees.

Deep exponential families for single-cell data.

Dynast Release ⭐ 11

Inclusive and efficient quantification of labeling and splicing RNAs for time-resolved metabolic labeling based scRNA-seq experiments

St_analysis ⭐ 8

A toolset for analysis and visualisation of Spatial Transcriptomics datasets.

A tool to quantify transposable elements expression in scRNA-seq

Python framework for single-cell RNA-seq clustering with special focus on transfer learning.

Cellregmap ⭐ 7

CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq

St_pipeline ⭐ 6

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

A simple python package for doublet detection in scRNA-seq data

MultiModal Classifier Hierarchy (MMoCHi)

Automated Sc Rna Seq Analysis In The Cloud ⭐ 5

scSPARKL is an Apache spark based pipeline for performing variety of preprocessing and downstream analysis of scRNA-seq data.

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