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325 search results found

Cellhint ⭐ 44

A tool for semi-automatic cell type harmonization and integration

Cell2cell ⭐ 44

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

Data toolkits for processing NMR, MALDI MSI, MALDI single cell, Raman Spectroscopy, LC-MS and GC-MS raw data, chemoinformatics data analysis and data visualization.

Scclustviz ⭐ 42

Explore and share your scRNAseq clustering results

Spicemix ⭐ 41

spatial transcriptome, single cell

Celltalker ⭐ 41

Inference of cell-cell communication from single-cell RNAseq data

Nsforest ⭐ 40

A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing

Iterative transfer learning with neural network improves clustering and cell type classification in single-cell RNA-seq analysis

Crosstalker ⭐ 39

R package to do the Ligand Receptor Analysis Visualization

Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.

Robust differential composition and variability analysis for single-cell data

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data

Scribe Py ⭐ 36

Regulatory networks with Direct Information in python

Experimental design framework for scRNAseq population studies (eQTL and DE)

Pcaworkshop ⭐ 35

An introduction to matrix factorization and PCA and SVD.

Identifying tumor cells at the single-cell level using machine learning

BRIE: Bayesian Regression for Isoform Estimate in Single Cells

Spatialtranscriptomics ⭐ 34

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Randomly ⭐ 33

A Library for Denoising Single-Cell Data with Random Matrix Theory

Meringue ⭐ 33

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

R package for pathway analysis in scRNA-seq data

VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

Sscclust ⭐ 32

simpler single cell RNAseq data clustering

Mouse cell atlas

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

Vitesscer ⭐ 32

R API and htmlwidget for Vitessce

Single-cell multi-omics integration using Optimal Transport

Cytomapper ⭐ 31

R package for visualization of highly multiplexed imaging data

Openproblems V2 ⭐ 31

Formalizing and benchmarking open problems in single-cell genomics

Cytometry Clustering Comparison ⭐ 30

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

An interface for Nested Stochastic Block Model for single cell analysis

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

Next-Gen Sequencing tools from the Horvath Lab

Descriptive probabilistic marker gene approach to single-cell pseudotime inference

Ot Scomics ⭐ 29

This Python package will allow you to replicate the experiments from our research on applying Optimal Transport as a similarity metric in between single-cell omics data.

Scnanogps ⭐ 29

Single cell Nanopore sequencing data for Genotype and Phenotype

Fastq_utils ⭐ 29

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

Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping

Csbb Shiny ⭐ 28

Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis

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

Vitessce Python ⭐ 28

Python API and Jupyter widget for Vitessce

scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference

Expressionmatrix2 ⭐ 27

Software for exploration of gene expression data from single-cell RNA sequencing.

Gcmodeller ⭐ 27

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Seuratv3wizard ⭐ 26

A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3

WebGL-based viewer for spatially-resolved transcriptomics data

Clonealign ⭐ 25

Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data

Split Seq_demultiplexing ⭐ 25

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

Scib Reproducibility ⭐ 25

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

ASAP : Automated Single-cell Analysis Pipeline

Scasat is a single cell ATAC-seq preprocessing and analysis pipeline

Tweedieverse ⭐ 24

Differential analysis of multi-omics data based on the Tweedie distribution

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

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.

Northstar ⭐ 23

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

Scopeloomr ⭐ 23

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...

Citefuse ⭐ 23

Beyondcell ⭐ 23

Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq data and proposing cancer-specific treatments.

Functional Associations using Variational Autoencoders

Scdeepcluster_pytorch ⭐ 22

Pytorch implementation of scDeepCluster for Single Cell RNA-seq data

Accurate and fast cell marker gene identification with COSG

A fast and accurate deconvolution algorithm based on regularized matrix completion algorithm (ENIGMA)

Imcdataanalysis ⭐ 22

R based workflow for multiplexed imaging data

Popsicler ⭐ 22

popsicleR, a flexible R package aimed at providing most of the necessary quality controls and preliminary information for complete and detailed analysis of single cell RNA-seq data.

Self-Supervised Vision Transformers for multiplexed imaging datasets

Spatially resolved transcriptomic analysis

Scgeatoolbox ⭐ 21

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

Cell2sentence Ft ⭐ 21

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

Mario Py ⭐ 21

MARIO: single-cell proteomic data matching and integration using both shared and distinct features

A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.

Non-parametric density inference for single-cell analysis.

Single-cell copy number calling and event history reconstruction.

Cshl Singlecell 2017 ⭐ 20

Single Cell Analysis course at Cold Spring Harbor Laboratory 2017

Scran.js ⭐ 19

Single cell analysis in Javascript

Seurat.utils ⭐ 19

Various utility functions for Seurat single-cell analysis

Python package for integrating and analyzing multiple single-cell datasets (A Python version of LIGER)

An analytics package for single cell data

Deepcycle ⭐ 19

Cell cycle inference in single-cell RNA-seq

Schicexplorer ⭐ 19

Single-cell Hi-C data analysis toolbox

Crop Seq ⭐ 19

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

Devcellpy ⭐ 18

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

Netsmooth ⭐ 18

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Tidygate ⭐ 18

Label elements within user drawn gates

Gchromvar ⭐ 18

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

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

Imcrtools ⭐ 18

An R package for handling and analysing imaging mass cytometry data

MeDuSA is a fine-resolution cellular deconvolution method that leverages scRNA-seq data as a reference to estimate cell-state abundance in bulk RNA-seq data.

Single cell proteomics data processing

Muto_wilson_ncomm_2020 ⭐ 17

Workflow for analysis of healthy human kidney by snRNAseq and snATACseq

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.

Torch Adata ⭐ 17

Create PyTorch Datasets from AnnData

Elefhant ⭐ 17

Ensemble Learning for Harmonization and Annotation of Single Cells (ELeFHAnt) provides an easy to use R package for users to annotate clusters of single cells, harmonize labels across single cell datasets to generate a unified atlas and infer relationship among celltypes between two datasets. It uses an ensemble of three machine learning classifiers 1) RF 2) SVM and 3) LR

Rpanglaodb ⭐ 17

An R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database into a Seurat object.

Low-dimensional Projection of Single Cell Velocity

SemI-SUpervised generative Autoencoder models for single cell data

Orange3 Single Cell ⭐ 16

🍊🔬 Orange add-on for gene expression of single cell data

Spatialtis ⭐ 16

Spatial analysis toolkit for single cell multiplexed tissue data

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