#Scrna-seq
Showing 21 of 21 repositories tagged #scrna-seq, ranked by stars
Deep probabilistic analysis of single-cell and spatial omics data
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
An interactive explorer for single-cell transcriptomics data
A tool for semi-automatic cell type classification
Useful functions to make your scRNA-seq plot more cool!
R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
Bring your single-cell data to life
Deep Embedding for Single-cell Clustering
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
A Snakemake workflow and MrBiomics module for performing and visualizing differential analyses of NGS data powered by the R package limma.
A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.
A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.
A Snakemake workflow and MrBiomics module for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) powered by the R package Seurat's method Mixscape.
A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
Examples using Clustergrammer2 to explore high-dimensional datasets.
Spatial Transcriptomics Dashboard
A toolset for analysis and visualisation of Spatial Transcriptomics datasets.
scBoolSeq: scRNA-Seq data binarisation and synthetic generation from Boolean dynamics