massonix
Postdoc in single-cell multiomics at Weill Cornell Medicine and New York Genome Center
WCM / NYGCNew York City
Pinned Repositories
cellranger
Scripts to create cellranger calls for multiple libraries of a subproject
code_snippets
A collection of code snippets for different tasks
HCATonsilData
Provide programmatic access to the tonsil cell atlas datasets
math_teaching
richter_transformation
Scripts scRNA-seq analysis Richter project
sampling_artifacts
Scripts and analysis notebook to reproduce all the scRNA-seq analysis in "Sampling time-dependent artifacts in single-cell genomics studies", published by Massoni-Badosa et al. in Genome Biology (2020)
SLOcatoR
SLOcatoR is an R package to annotate single-cell transcriptomes and open chromatin profiles from secondary lymphoid organs using the tonsil atlas as reference
tabula_muris_networks
R markdown notebooks for the Tabula Muris network analysis in Iacono et al. (2019)
TonsilAtlas
Scripts and notebooks to reproduce all analysis from Massoni-Badosa et al. (2022)
TonsilAtlasCAP
Scripts to document how to get the tonsil atlas dataset ready to upload to the cell annotation platform (CAP)
massonix's Repositories
massonix/tabula_muris_networks
R markdown notebooks for the Tabula Muris network analysis in Iacono et al. (2019)
massonix/code_snippets
A collection of code snippets for different tasks
massonix/HCATonsilData
Provide programmatic access to the tonsil cell atlas datasets
massonix/sampling_artifacts
Scripts and analysis notebook to reproduce all the scRNA-seq analysis in "Sampling time-dependent artifacts in single-cell genomics studies", published by Massoni-Badosa et al. in Genome Biology (2020)
massonix/richter_transformation
Scripts scRNA-seq analysis Richter project
massonix/SLOcatoR
SLOcatoR is an R package to annotate single-cell transcriptomes and open chromatin profiles from secondary lymphoid organs using the tonsil atlas as reference
massonix/TonsilAtlasCAP
Scripts to document how to get the tonsil atlas dataset ready to upload to the cell annotation platform (CAP)
massonix/cellranger
Scripts to create cellranger calls for multiple libraries of a subproject
massonix/Massomics
Massomics: home of single-cell genomics education
massonix/math_teaching
massonix/cellranger_hashing
Scripts to create cellranger calls in scRNA-seq experiments that include cell hashing
massonix/cluster_scripts
Scripts to run computer-intensive operations in the cluster
massonix/TonsilAtlas
Scripts and notebooks to reproduce all analysis from Massoni-Badosa et al. (2022)
massonix/bulk_genomics_2024
This repository contains a 2024 version of how to run end-end buk genomics / transcriptomics / epigenomics analysis
massonix/cv-1
My Curriculum Vitae
massonix/depreacted_SLOcatoR
massonix/epid_20
massonix/FERRER_07
massonix/Python-project
massonix/RICHTER
massonix/rosalind_problems
My solutions to the bioinformatics problems in rosalind.info
massonix/SBI-project
massonix/SBI-project-1
SBI-Python project , Constructing macromolecular complexes.
massonix/symphony
Efficient and precise single-cell reference atlas mapping with Symphony
massonix/TabulaMurisSenisData
data from the TabulaMuris Senis project
massonix/Tbet_in_CLL
TBET expression and activity in tonsillar cells; in the context of a larger project looking at TBET expression in chronic lymphocytic leukemia (CLL)
massonix/test
test