Alternatives and similar repositories for st_pipeline:

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

• SpatialTranscriptomicsResearch / st_pipeline
  ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …
  ☆82Updated 3 years ago
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆102Updated last year
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆61Updated 2 years ago
• MingyuYang-Yale / DBiT-seq
  ☆22Updated 2 years ago
• tiroshlab / 3ca
  Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".
  ☆92Updated 5 months ago
• YMa-lab / CARD
  ☆105Updated last year
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆96Updated 2 weeks ago
• Japrin / STARTRAC
  STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)
  ☆94Updated last year
• YosefLab / popV
  ☆69Updated last week
• navinlabcode / CellTrek
  ☆114Updated 2 years ago
• saezlab / visium_heart
  Spatial transcriptomics of heart tissue
  ☆80Updated last year
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆59Updated last month
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆86Updated 6 months ago
• quadbio / scMultiome_analysis_vignette
  Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
  ☆54Updated 9 months ago
• YosefLab / Compass
  In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
  ☆106Updated 3 weeks ago
• zhengrongbin / MEBOCOST
  A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data
  ☆71Updated 3 months ago
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆77Updated 2 months ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆100Updated 5 months ago
• theislab / spatial_scog_workshop_2022
  Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
  ☆52Updated 2 years ago
• cellgeni / schard
  reticulate-free single cell format conversion
  ☆124Updated 2 months ago
• Sijin-ZhangLab / PanMyeloid
  ☆98Updated 4 years ago
• matanhofree / crc-immune-hubs
  Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organiz…
  ☆39Updated 3 years ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆59Updated 8 months ago
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆83Updated 7 months ago
• tanlabcode / spatial-bonemarrow-atlas
  This repository contains the code used to generate figures and perform analysis for the manuscript titled "Transcriptomic and Spatial Pro…
  ☆73Updated 4 months ago
• 10XGenomics / HumanColonCancer_VisiumHD
  Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…
  ☆46Updated this week
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆121Updated this week
• ShellyCoder / cellcall
  inferring cell-cell communication from scRNA-seq of ligand-receptor
  ☆77Updated last year
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆39Updated 3 years ago
• carmonalab / GeneNMF
  Methods to discover gene programs on single-cell data
  ☆100Updated 3 months ago