Pinned Repositories
COVID19
A worldwide epidemiological database for COVID-19 at fine-grained spatial resolution
Bayesian-for-BOLD
Using a two-step bayesian framework to model ground truth BOLD signal
BC2_Spatial_Transcriptomics
Discrete-vs-Continuous-MSM
Modeling pharmacoepidemiological dispensation data as a multiple visit marked point process
EstellaD
My Bio
ggspavis
Visualization functions for spatially resolved transcriptomics data
mosaic_pilot_study
A repo hosting scirpts to reproduce the analyses in the manuscript.
OSTA.data
OSTA book loading data from Open Science Framework to cache or local download.
SpatialExperimentIO
Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
SpatialTranscriptomicsWorkflow
Foundation to the upcoming workflow chapters in the BestPracticesST book https://lmweber.org/BestPracticesST/
estellad's Repositories
estellad/SpatialExperimentIO
Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
estellad/SpatialTranscriptomicsWorkflow
Foundation to the upcoming workflow chapters in the BestPracticesST book https://lmweber.org/BestPracticesST/
estellad/Discrete-vs-Continuous-MSM
Modeling pharmacoepidemiological dispensation data as a multiple visit marked point process
estellad/EstellaD
My Bio
estellad/OSTA.data
OSTA book loading data from Open Science Framework to cache or local download.
estellad/Bayesian-for-BOLD
Using a two-step bayesian framework to model ground truth BOLD signal
estellad/BC2_Spatial_Transcriptomics
estellad/BinXenium
estellad/BiocStickers
Stickers for some Bioconductor packages - feel free to contribute and/or modify.
estellad/Conv-EEG-Decoding
Decoding EEG signals using Convolutional Neural Networks
estellad/GeoMXAnalysisWorkflow
GeoMX analysis workflow
estellad/ggspavis
Visualization functions for spatially resolved transcriptomics data
estellad/mosaic_pilot_study
A repo hosting scirpts to reproduce the analyses in the manuscript.
estellad/SeuratQCUtils
Automate single-cell resolution QC of any Seurat single-cell or spatial object.
estellad/gggroupedscale
Grouped Discrete Scale for 'ggplot2'
estellad/multiomics-data-analysis-and-integration-training
estellad/plotOnUMAP
Plot UMAP colored by continuous feature expression level or by categorical clusters
estellad/PrinciplesSTA
"Principles of Spatial (Transcript)omics Analysis with Bioconductor" book
estellad/sc-SHC
Significance analysis for clustering single-cell RNA-sequencing data
estellad/shinySTRegister
estellad/SpaceHack2023
estellad/spacexr
Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
estellad/SpatialData
estellad/SpatialExperiment
estellad/SpatialExperimentIOData
Some toy example data for demonstration of other packages and workflows
estellad/STalign_test
estellad/STexampleData
Collection of spatially resolved transcriptomics datasets in SpatialExperiment R/Bioconductor format
estellad/transformGamPoi-Paper
estellad/VIB_Hackathon_June_2024
Code repository for the VIB Hackathon June 2024 on spatial omics. More info: https://hackmd.io/@berombau/BJetSxw8T
estellad/XeniumPreprintBreastCancerData
Xenium preprint data shared on ExperimentHub