caramirezal
Data Scientist and music lover.
Health Data Science Unit, Heidelberg UniversityINF 267, 69120 Heidelberg
Pinned Repositories
dataScience
This repository contains documentation and scripts for programming, mathematical modeling, machine learning, and data science courses.
Drop-seq
Java tools for analyzing Drop-seq data
hcv_scDataIntegration
Projection of scRNA-seq data on hematopoietic cells from hepatitis C virus infected patients on scRNA-seq and scATAC-seq of immune cell profiles.
interaction_DC-pathogens
Analysis of the gene expression changes during Dendritic cell interaction with pathogens at the single cell level.
sars-cov2
Single cell data analysis of ACE2 and TMPRSS2 COVID-19 receptors expression on multiple tissues.
single-Cell_RNA-Seq_pipeline
Illumina Bio-Rad Single-Cell Sequencing workflow
singleCellDeconvolution
The aim of this project is to combine multiple single cell layers of information into a unified framework projecting a reference into a query data base and then applying a non-negative matrix factorization in order to assess the behavior of the regulatory fluxes.
SNARE_prep
dropseq-based single nuclei genomic accessibility and RNA expression (SNARE-seq) preprocessing pipeline
SQUADBookChapter
Dynamic network models has been used in biological contexts to represent complex regulatory interactions between molecules. Discrete Boolean methods are often used as a first modeling approximation. However in some biological contexts they are not sufficient to represent some behaviors as that which depends on threshold activation or molecular gradients. In these cases, ordinary differential equations are preferred but their application need the knowledge of kinetic parameters. Here we describe a continuous ODE system called Standardized Qualitative Analysis of Dynamics (SQUAD) as a first approximation to simulate continuous models without the need of kinetic parameters.
caramirezal's Repositories
caramirezal/sars-cov2
Single cell data analysis of ACE2 and TMPRSS2 COVID-19 receptors expression on multiple tissues.
caramirezal/dataScience
This repository contains documentation and scripts for programming, mathematical modeling, machine learning, and data science courses.
caramirezal/interaction_DC-pathogens
Analysis of the gene expression changes during Dendritic cell interaction with pathogens at the single cell level.
caramirezal/Drop-seq
Java tools for analyzing Drop-seq data
caramirezal/hcv_scDataIntegration
Projection of scRNA-seq data on hematopoietic cells from hepatitis C virus infected patients on scRNA-seq and scATAC-seq of immune cell profiles.
caramirezal/singleCellDeconvolution
The aim of this project is to combine multiple single cell layers of information into a unified framework projecting a reference into a query data base and then applying a non-negative matrix factorization in order to assess the behavior of the regulatory fluxes.
caramirezal/SNARE_prep
dropseq-based single nuclei genomic accessibility and RNA expression (SNARE-seq) preprocessing pipeline
caramirezal/ATAC-Seq
Snake pipeline for the alignment of ATAC-Seq data.
caramirezal/Bayesian-Correlations
caramirezal/bioinformatics-tools
Snakemake workflow containing a collection of bioinformatics tools.
caramirezal/caramirezal.github.io
This web site contains my personal software projects
caramirezal/dropSeqPipe
A SingleCell RNASeq pre-processing snakemake workflow
caramirezal/floJoVIHDataAnalysis
Data analysis on cytometry data from samples of VIH patients.
caramirezal/gitTutorial
Git tutorial and practice.
caramirezal/liver_spatial_atlas
Definition of an integrated atlas of spatial transcriptomics of the liver
caramirezal/monocle-release
caramirezal/multiome_ifn_project
This repository contains the analysis of multiomic GEX + ATAC Seq data of human cells treated/untreated with IFN, polyIC or dsRNA at different time points. The aim of this project is to study Genetic Regulatory Networks (GRN).
caramirezal/multiomics
This repository contains algorithms to analyse single cell multomic data.
caramirezal/neuroblastoma
Integrative single cell data analysis
caramirezal/obesity
Here, we analyze the relationship of immune cells and inflammatory responses with obesity using data based on a cohort of eutrofic and obese patients.
caramirezal/pipelines-scRNAseq
This repository contains a snakemake pipe for the automation of scRNA-Seq routines used for the HDSU lab in the curry cluster.
caramirezal/rocketVI
A repository for deep learning models exploration and testing
caramirezal/SATSNE2019
R code for Soft Alignment of t-SNEs
caramirezal/scRNASeq_lung
Data preprocessing and analysis of scRNASeq data of lung cells treated with IFN.
caramirezal/severity-markers-regulation
Evaluation of the possible co-regulation of markers associated to severity in SARS-CoV2.
caramirezal/shinnyapps
Testing shiny apps
caramirezal/snare_pipe
Processing scATAC-Seq data for integration to scRNA-Seq data.
caramirezal/tcd8ExscSeq
Analysis of cell signatures in T CD8 Exhausted cells in scRNA and scATAC-Seq.
caramirezal/tissueSpecificRegulonInference
Integration of scRNA- and bulk ATAC-Seq data to refine TF regulon reconstruction.
caramirezal/vihCohort
The aim of this study is to find predictors for the appearence of Immune Reconstitution Inflammatory Syndrome (IRIS) in patients treated con antiretroviral therapy (ART).