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bulk_genomics_2024

This repository contains a 2024 version of how to run end-end buk genomics / transcriptomics / epigenomics analysis

cellranger

Scripts to create cellranger calls for multiple libraries of a subproject

cellranger_hashing

Scripts to create cellranger calls in scRNA-seq experiments that include cell hashing

cluster_scripts

Scripts to run computer-intensive operations in the cluster

code_snippets

A collection of code snippets for different tasks

cv-1

My Curriculum Vitae

depreacted_slocator

epid_20

ferrer_07

hcatonsildata

Provide programmatic access to the tonsil cell atlas datasets

massomics

Massomics: home of single-cell genomics education

math_teaching

python-project

richter

richter_transformation

Scripts scRNA-seq analysis Richter project

rosalind_problems

My solutions to the bioinformatics problems in rosalind.info

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)

sbi-project

sbi-project-1

SBI-Python project , Constructing macromolecular complexes.

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

symphony

Efficient and precise single-cell reference atlas mapping with Symphony

tabula_muris_networks

R markdown notebooks for the Tabula Muris network analysis in Iacono et al. (2019)

tabulamurissenisdata

data from the TabulaMuris Senis project

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)

test

test

tonsilatlas

Scripts and notebooks to reproduce all analysis from Massoni-Badosa et al. (2022)