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Search results for single cell scrna seq

42 search results found

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Scrna Seq_notes ⭐ 478

A list of scRNA-seq analysis tools

Scrna Tools ⭐ 295

Table of software for the analysis of single-cell RNA-seq data.

Scarches ⭐ 294

Reference mapping for single-cell genomics

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

Single cell perturbation prediction

Celltypist ⭐ 202

A tool for semi-automatic cell type classification

Single Cell Papers With Code ⭐ 193

Papers with code for single cell related papers

Pagoda2 ⭐ 191

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

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

Sccustomize ⭐ 142

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

Scdeepsort ⭐ 93

Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

Cirrocumulus ⭐ 63

Bring your single-cell data to life

Demultiplexing pooled scRNA-seq data with or without genotype reference

Dynverse ⭐ 58

A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍

Cardelino ⭐ 57

Clone identification from single-cell data

Scperturb ⭐ 56

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

Multinichenetr ⭐ 56

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

single cell Flux Estimation Analysis (scFEA) Try the below web server!

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

Scclustviz ⭐ 42

Explore and share your scRNAseq clustering results

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.

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

Fastq_utils ⭐ 29

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

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

Scib Reproducibility ⭐ 25

Additional code and analysis from the single-cell integration benchmarking project

Split Seq_demultiplexing ⭐ 25

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

Northstar ⭐ 23

Single cell type annotation guided by cell atlases, with freedom to be queer

BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.

Scgeatoolbox ⭐ 21

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

Cell2sentence Ft ⭐ 21

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

Devcellpy ⭐ 18

devCellPy is a Python package designed for hierarchical multilayered classification of cells based on single-cell RNA-sequencing.

Cell type matching in single-cell RNA-sequencing data using FR-Match

R package developed for single-cell RNA-seq analysis. It was designed using the Seurat framework, and offers existing and novel single-cell analytic work flows.

Bgeedb_r ⭐ 13

Source code of the R packge BgeeDB to use data from the Bgee database

Clustermole ⭐ 11

Unbiased single-cell transcriptomic data cell type identification

Topicvelo ⭐ 11

TopicVelo: Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems

Apackoftheclones ⭐ 10

Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles.

A tool to quantify transposable elements expression in scRNA-seq

Characterize gene dynamics over trajectories using GLMs, GEEs, & GLMMs.

Dea_seurat ⭐ 6

A Snakemake workflow for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.

Neuroblastoma ⭐ 6

Single-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis

Single Cell RNA-seq UMI Filtering Facilitator

IKAP - Identifying K mAjor cell Population groups in single-cell RNA-seq analysis

Scdeepsort_performance_comparison ⭐ 5

The source code and results for different methods on annotating external testing datsets of human and mouse.

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