John Pablo Mendieta 's starred repositories
Terminators-Plant-STARR-seq
Code and data for Plant Terminators STARR-seq
tfmodisco-lite
A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
chrombpnet
Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
dragonnfruit
A method for analyzing scATAC-seq experiments.
neural_motif_discovery
Framework for interrogating transcription-factor motifs and their syntax/grammars from neural-network interpretations
tangermeme
Biological sequence analysis for the modern age.
PanEffect
PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) explore all possible amino acid substitutions and their variant effects for a reference genome, and (2) view the natural variation and their effects across a pangenome.
StructuralVariation_ShinyApp
Scripts Related to R Shiny App Visualizing Structural Variation Identified Using AnchorWave
PolymorphicTEs_NAM
Code Used To Call Polymorphic TEs between B73 and the remaining 25 Nested Association Mapping Lines
Conservatory
Identification of conserved non-coding sequences in plants
scHierarchy
A toolking for cell type hierarchies: marker selection & consistent classification
stat_rethinking_2022
Statistical Rethinking course winter 2022
neutral-model-estimator
Simple pipeline to go from an alignment to a neutral model, using the PHAST toolkit
awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
SnakeRNASeq
A Snakemake workflow to process paired-end RNA-Seq data.
CutNRun_2021
scripts from "High resolution profiling of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&TAG"