Alternatives and similar repositories for visium_stitcher

Users that are interested in visium_stitcher are comparing it to the libraries listed below

• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆40Updated last month
• Teichlab / snp2cell
  cell type specific, trait-associated gene regulation
  ☆27Updated 4 months ago
• jbergenstrahle / STUtility
  ☆52Updated 2 years ago
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆73Updated 9 months ago
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆28Updated 8 months ago
• AllenInstitute / scrattch.bigcat
  iterative clustering pipeline of big single cell datasets.
  ☆33Updated 3 months ago
• UPSUTER / GEMLI
  ☆32Updated 6 months ago
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆61Updated last year
• zijianni / SpotClean
  R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
  ☆32Updated last year
• NBISweden / single-cell_sib_scilifelab
  SIB/Scilifelab autumn school in single cell omics 2019.
  ☆22Updated 5 years ago
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆19Updated last year
• kharchenkolab / cacoa
  Single-cell Case Control Analysis
  ☆51Updated 8 months ago
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆27Updated last year
• ZJUFanLab / CellTalkDB
  A manually curated database of literature-supported ligand-receptor interactions in human and mouse
  ☆31Updated last year
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆38Updated 2 months ago
• Janezjz / cellanova
  CellANOVA: Cell State Space Analysis of Variance for signal recovery in single cell batch integration
  ☆49Updated 9 months ago
• JEFworks-Lab / veloviz
  RNA-velocity informed embeddings for visualizing cellular trajectories
  ☆44Updated 2 years ago
• Teichlab / sctk
  ☆40Updated this week
• veltenlab / CloneTracer
  This repository contains scripts to identify healthy and malignant cells from scRNAseq with CloneTracer and process data from Optimized 1…
  ☆26Updated 9 months ago
• edsgard / trendsceek
  Identify genes with spatial expression trends in single-cell gene expression data
  ☆51Updated 7 years ago
• MagpiePKU / EpiTrace
  Cell age determination by scATAC-seq and bulk-ATAC-seq
  ☆32Updated 11 months ago
• dyxmvp / Spatial_ATAC-seq
  ☆22Updated 2 years ago
• kaishumason / NicheDE
  NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.
  ☆20Updated last month
• lijxug / CSOmapR
  R package of CSOmap(developing
  ☆14Updated 3 years ago
• rargelaguet / mouse_organogenesis_10x_multiome_publication
  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""
  ☆40Updated 2 years ago
• GreenleafLab / brainchromatin
  Code used to analyze single cell RNA and ATAC sequencing in developing human brain
  ☆33Updated 3 years ago
• Nanostring-Biostats / SpatialDecon
  The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This al…
  ☆40Updated 2 months ago
• Winnie09 / Lamian
  ☆55Updated last year
• morris-lab / CellTagR
  This repository contains the CellTag data analysis R package to support clone calling and lineage reconstruction.
  ☆21Updated 2 years ago
• saeyslab / spotless-benchmark
  A repository for benchmarking spatial deconvolution and mapping tools
  ☆33Updated 2 months ago