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
• MingyuYang-Yale / DBiT-seq
  ☆23Updated 3 weeks ago
• Japrin / STARTRAC
  STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)
  ☆96Updated last year
• quadbio / scMultiome_analysis_vignette
  Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
  ☆54Updated 11 months ago
• YosefLab / popV
  ☆71Updated this week
• navinlabcode / CellTrek
  ☆115Updated 2 years ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆100Updated last month
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆100Updated 6 months ago
• tiroshlab / 3ca
  Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".
  ☆98Updated 6 months 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
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆62Updated 2 years ago
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆72Updated 7 months ago
• theislab / spatial_scog_workshop_2022
  Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
  ☆53Updated 2 years ago
• saezlab / visium_heart
  Spatial transcriptomics of heart tissue
  ☆81Updated last year
• YMa-lab / CARD
  ☆110Updated last year
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆40Updated 3 years ago
• LocasaleLab / Single-Cell-Metabolic-Landscape
  Pipeline for exploring metebolic heterogeneity at single-cell resolution
  ☆74Updated 5 years ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆66Updated last week
• swaruplab / Single-nuclei-epigenomic-and-transcriptomic-landscape-in-Alzheimer-disease
  Single-nuclei RNA-seq and ATAC-seq in Alzheimer's disease
  ☆93Updated 3 years ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆140Updated 3 years ago
• carmonalab / GeneNMF
  Methods to discover gene programs on single-cell data
  ☆105Updated this week
• zhengrongbin / MEBOCOST
  A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data
  ☆71Updated 4 months ago
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆97Updated this week
• TheHumphreysLab / plot1cell
  ☆104Updated 2 weeks ago
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆84Updated 8 months ago
• digitalcytometry / cytotrace2
  CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.
  ☆126Updated last month
• icbi-lab / luca
  Single-cell Lung Cancer Atlas with 1.2M cells
  ☆60Updated 2 months ago
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆113Updated 6 months ago
• ShellyCoder / cellcall
  inferring cell-cell communication from scRNA-seq of ligand-receptor
  ☆78Updated last year