nf-core / spatialviLinks
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
☆70Updated this week
Alternatives and similar repositories for spatialvi
Users that are interested in spatialvi are comparing it to the libraries listed below
Sorting:
- A repository of pipelines for single-cell data in Nextflow DSL2☆80Updated 2 years ago
- ☆49Updated this week
- Tools for single-cell data processing☆131Updated last year
- R implementation of MULTI-seq sample classification workflow☆65Updated 2 years ago
- Single Cell Analysis of Five'Ends☆50Updated last year
- UniverSC: a flexible cross-platform single-cell data processing pipeline☆46Updated last year
- Finding gene expression states in scRNA-seq data☆50Updated last year
- A single cell transcriptomics pipeline for QC, integration and making the data presentable☆83Updated this week
- mutation(barcode) caller for 10x single cell data☆44Updated 5 years ago
- ☆59Updated last year
- ☆82Updated 2 years ago
- kallisto | bustools workflow for pre-processing single-cell RNA-seq data☆119Updated 3 years ago
- A single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic …☆82Updated 8 months ago
- SNV calling from single cell sequencing☆118Updated last year
- Pileup biallelic SNPs from single-cell and bulk RNA-seq data☆82Updated 3 years ago
- scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two cond…☆43Updated 2 years ago
- ☆46Updated 2 months ago
- mgatk: mitochondrial genome analysis toolkit☆110Updated last year
- Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…☆110Updated 2 months ago
- scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics☆57Updated last year
- Filtering of Poison noise on a single-cell RNA-seq UMI count matrix☆77Updated last month
- ☆23Updated 5 years ago
- A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data☆81Updated 3 weeks ago
- A tool that allows to get UMI counts from a single cell protein assay☆87Updated 9 months ago
- Genomic coordinates of problematic genomic regions as GRanges☆51Updated last month
- This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL☆56Updated 2 years ago
- A method to rapidly assess cell type identity using both functional and random gene sets☆39Updated last year
- A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…☆58Updated 4 years ago
- Efficient genotyping bi-allelic SNPs on single cells☆156Updated 3 months ago
- Discover differential transcript usage from polyA-captured single cell RNA-seq data☆53Updated 2 years ago