Pinned Repositories
sccomp
Mixed-effect model to test differences in cell type proportions from single-cell data, in R
bioc_2020_tidytranscriptomics
Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap
CuratedAtlasQueryR
Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
nanny
A tidyverse suite for (pre-) machine-learning: cluster, PCA, permute, impute, rotate, redundancy, triangular, smart-subset, abundant and variable features.
tidybulk
Brings bulk and pseudobulk transcriptomics to the tidyverse
tidygate
Label elements within user drawn gates
tidyHeatmap
Draw heatmap simply using a tidy data frame
tidyseurat
Seurat meets tidyverse. The best of both worlds.
tidySingleCellExperiment
Brings SingleCellExperiment objects to the tidyverse
tidySummarizedExperiment
Brings SummarizedExperiment to the tidyverse
stemangiola's Repositories
stemangiola/tidyHeatmap
Draw heatmap simply using a tidy data frame
stemangiola/tidybulk
Brings bulk and pseudobulk transcriptomics to the tidyverse
stemangiola/tidyseurat
Seurat meets tidyverse. The best of both worlds.
stemangiola/CuratedAtlasQueryR
Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
stemangiola/tidySingleCellExperiment
Brings SingleCellExperiment objects to the tidyverse
stemangiola/nanny
A tidyverse suite for (pre-) machine-learning: cluster, PCA, permute, impute, rotate, redundancy, triangular, smart-subset, abundant and variable features.
stemangiola/tidySummarizedExperiment
Brings SummarizedExperiment to the tidyverse
stemangiola/tidygate
Label elements within user drawn gates
stemangiola/ppcseq
Probabilistic outlier identification for bulk RNA sequencing data
stemangiola/tidysc
[Not ready for third party use] A modular framework and a tidy data structure for bulk transcriptional analyses.
stemangiola/infiltrating_immune_dataset
Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
stemangiola/singh_et_al_taurine_bone
stemangiola/single_cell_outliers
stemangiola/cellsig
stemangiola/cellxgenedp
R interface to the cellxgene data portal
stemangiola/Banksy
BANKSY: spatial clustering
stemangiola/biocblog
A Quarto blog for Bioconductor community
stemangiola/brms
brms R package for Bayesian generalized multivariate non-linear multilevel models using Stan
stemangiola/conferenceWiki
Centerlized Location for Bioconductor Conference materials, templates, and resources
stemangiola/glmmSeq
Gene-level general linear mixed model
stemangiola/instantiate
Pre-compiled CmdStan models in R packages
stemangiola/mangiola_et_al_2025_breast_cancer_pbmc
stemangiola/sccomp_ARCHIVE
Mixed-effect model to test differences in cell type proportions from single-cell data, in R
stemangiola/shiny_immune_map_results
This is a repository that include the data necessary to build a shiny app to dynamically communicate the results of our immune map paper
stemangiola/squidr
Use squidpy through R
stemangiola/SubcellularSpatialData
This repository hosts a data package with annotated sub-cellular resolution spatial transcriptomics datasets.
stemangiola/tidyomicsWorkshop_ECCB2024
Tidy genomic and transcriptomic analyses
stemangiola/tidySpatialExperiment
Brings SpatialExperiment to the Tidyverse
stemangiola/ttservice
stemangiola/turrr
Apply Mapping Functions in Parallel using Targets