Alternatives and similar repositories for scPagwas

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

• karthikj89 / scgenetics
  identifying disease critical cell types and programs from single cell RNAseq
  ☆57Updated 3 years ago
• swaruplabUCI / ArchRtoSignac
  An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)
  ☆36Updated 11 months ago
• Jiaxin-Fan / MuSiC2
  cell type deconvolution for multi-condition bulk RNA-seq data
  ☆27Updated 3 years ago
• smorabit / hdWGCNA_paper
  Code used to run the data analysis in the hdWGCNA manuscript (Morabito et al 2022)
  ☆16Updated 2 years ago
• immunogenomics / SCENT
  Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA
  ☆77Updated 3 months ago
• jbryois / scRNA_disease
  Code for our paper: https://www.biorxiv.org/content/10.1101/528463v1
  ☆18Updated 5 years ago
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆73Updated 9 months ago
• phillipnicol / scDist
  Robust identification of perturbed cell types in single-cell RNA-seq data
  ☆32Updated 8 months ago
• perslab / CELLEX
  CELLEX (CELL-type EXpression-specificity)
  ☆43Updated 2 years ago
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆75Updated 11 months ago
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆29Updated 8 months ago
• SGDDNB / GeneSwitches
  Ordering gene-expression and functional events in single-cell experiments
  ☆22Updated last year
• kkdey / GSSG
  Gene Set + S2G strategy annotations analyzed for disease architecture
  ☆53Updated 2 years ago
• qingnanl / gsdensity
  ☆9Updated last year
• jumphone / Vector
  Unsupervised Inference of Developmental Directions for Single Cells
  ☆22Updated last year
• Teichlab / snp2cell
  cell type specific, trait-associated gene regulation
  ☆27Updated 4 months ago
• gxiaolab / scAllele
  ☆37Updated last year
• hernet / transcriptional-map-nk
  We describe a transcriptional reference map of human natural killer (NK) cells based on analysis of scRNA-seq data from both blood and ti…
  ☆11Updated 10 months ago
• Coolgenome / PDAC
  ☆18Updated 5 months ago
• gabrielakinker / CCLE_heterogeneity
  ☆58Updated last year
• abelson-lab / scATOMIC
  Pan-Cancer Single Cell Classifier
  ☆74Updated last year
• sunnyzwu / stromal_subclasses
  code for data processing and visualisation associated with the stromal subclasses manuscript
  ☆11Updated 4 years ago
• dengchunyu / scPagwas
  Obtain trait-relevant cell subpopulations by incorporating pathway activity transformed scRNA-seq data with GWAS data
  ☆17Updated 8 months ago
• AllenInstitute / scrattch.bigcat
  iterative clustering pipeline of big single cell datasets.
  ☆33Updated 3 months ago
• tiroshlab / Spatial_Glioma
  Code for major analyses in "Integrative spatial analysis reveals a multi-layered organization of glioblastoma" paper
  ☆49Updated 7 months ago
• aet21 / SCENT
  Estimation of Single-Cell Potency with Single Cell Entropy
  ☆42Updated 2 years ago
• NathanSkene / EWCE
  Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.
  ☆59Updated 5 months ago
• immunogenomics / sceQTL
  Code for single-cell eQTL analysis of memory T cell data in Nathan, et al. bioRxiv (2021)
  ☆20Updated 2 years ago
• guangchunhan / LUAD_Code
  ☆21Updated last year
• immunogenomics / GeNA
  Genotype-Neighborhood Associations: A tool for identifying genetic variant associations to the abundance of cell states in single-cell d…
  ☆14Updated 10 months ago