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 …
  ☆84Updated 4 years ago
• navinlabcode / CellTrek
  ☆129Updated 3 years ago
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆117Updated 2 months ago
• tiroshlab / 3ca
  Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".
  ☆131Updated last year
• icbi-lab / luca
  Single-cell Lung Cancer Atlas with 1.2M cells
  ☆86Updated last year
• quadbio / scMultiome_analysis_vignette
  Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
  ☆68Updated last year
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆127Updated 8 months ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆106Updated last year
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆153Updated 3 years ago
• Swarbricklab-code / BrCa_cell_atlas
  Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".
  ☆125Updated last year
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆138Updated 11 months ago
• YMa-lab / CARD
  ☆129Updated last year
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆88Updated 3 years ago
• MingyuYang-Yale / DBiT-seq
  ☆25Updated 11 months ago
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆143Updated 2 years ago
• YosefLab / popV
  ☆87Updated this week
• YosefLab / Compass
  In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
  ☆120Updated 3 months ago
• ShobiStassen / VIA
  trajectory inference
  ☆105Updated last year
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆134Updated 3 months ago
• theislab / spatial_scog_workshop_2022
  Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
  ☆53Updated 3 years ago
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆182Updated last year
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆80Updated last year
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆123Updated last year
• Japrin / STARTRAC
  STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)
  ☆115Updated 9 months ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆79Updated this week
• GreenleafLab / 10x-scATAC-2019
  Publication Page for Satpathy*, Granja* et al 2019
  ☆94Updated 5 years ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆84Updated 10 months ago
• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆113Updated 3 years ago
• LocasaleLab / Single-Cell-Metabolic-Landscape
  Pipeline for exploring metebolic heterogeneity at single-cell resolution
  ☆75Updated 5 years ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆107Updated 2 years ago