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Search results for single cell transcriptomics

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28 search results found

Pyscenic ⭐ 321

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

Single cell perturbation prediction

Pagoda2 ⭐ 191

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

Sccatch ⭐ 171

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

R package for analyzing single-cell RNA-seq data

Alevin Fry ⭐ 115

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

Decoupler Py ⭐ 112

Python package to perform enrichment analysis from omics data.

Scdeepsort ⭐ 93

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

Multiome GRN inference.

Singlecellhaystack ⭐ 68

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

Multi-sample Unified Discriminant ANalysis

Cirrocumulus ⭐ 63

Bring your single-cell data to life

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

Celltalker ⭐ 41

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

Spatialtranscriptomics ⭐ 34

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

R package for pathway analysis in scRNA-seq data

ASAP : Automated Single-cell Analysis Pipeline

Omicssuite.github.io ⭐ 15

OmicsSuite website for releasing new version.

SCASA: Single cell transcript quantification tool

Topicvelo ⭐ 11

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

Molecular interactions inference from single-cell multi-omics data

Singlecellhaystack Py ⭐ 8

Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).

Materials used during #NGSchool2017

Iteratively Adjusted Surrogate Variable Analysis

Trendcatcher ⭐ 7

TrendCatcher is an open source R-package that allows users to systematically analyze and visualize time course data. Please cite "Temporal transcriptomic analysis using TrendCatcher identifies early and persistent neutrophil activation in severe COVID-19" by Xinge Wang et al published in JCI Insight (2022) - https://insight.jci.org/articles/view/157255

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

Perform differential transcript usage (DTU) analysis of bulk or single-cell RNA-seq data. See documentation at:

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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1-28 of 28 search results

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