Pedro Madrigal's repositories
neMeRIP-seq
Scripts for neMeRIP-seq data analysis
bioinformatics-pipeline-tutorial
A tutorial on how to create bioinformatics pipelines as bash scripts, Makefiles and using tools like Nextflow.
bioinformatics-training-collection
Collection of bioinformatics training materials
bivariate-genomic-footprinting
Scripts to run footprinting and motif-flanking accessibility analysis in DNase-seq/ ATAC-seq data
jenkins-pipeline-examples
A collection of examples, tips and tricks and snippets of scripting for the Jenkins Pipeline plugin
KLTepigenome
Uncovering correlated variability in epigenomic datasets using the Karhunen-Loeve Transform
spatial_scog_workshop_2022
Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
bioconductor-ci-validator
Bioconductor package validator via Continuous Integration
xml-validator
XML format validator in Julia Lang
ansible-role-solr
Ansible Role - Apache Solr
bioconda-recipes
Conda recipes for the bioconda channel.
cellranger-vdj
V(D)J T Cell and B Cell Analysis with cellranger vdj
dosymetric-image-reconstruction
Reconstructing dosimetric images using a deconvoluted physical model
hands-on-llms
A practical workshop to how large language model systems work, and how to get up and running quickly.
json-validate
JSON validator in bash
lncrna-genelab-atlas
Detection of long non-coding RNAs (lncRNAs) during Spaceflight using RNA-seq data
mams
Matrix and Analysis Metadata Standards
patterns
A curated collection of Nextflow implementation patterns -- http://nextflow-io.github.io/patterns/index.html
RandomForest
A simple example of a Random-Forest classifier
rmams
R package for Matrix and Analysis Metadata Standards
rnacentral-webinar
Jupyter notebooks to run interactive parts of the RNAcentral webinar
sc-lymphomagenesis
A single-cell atlas of lymphoma evolution
scatlas_ontology
SCA_Ontology
sparseSingleCell
Scripts for the analysis of single-cell epigenomics data using Sparse-FDA