John Pablo Mendieta 's repositories
Augustus_Training
Scripts to train augustus software using PASA pipeline output files.
MendietaPablo_Annotation_Paper_scripts
Scripts used for analysis and pipline of Mendieta et al 2020
Annotation-Tools
Scripts and tools to assist annotation.
BioinformaticsScripts
An improved Repo of usful scrips for various scripts I have designed to work with NGS data. Scripts are free to use
biopython
Official git repository for Biopython (converted from CVS)
containers
Bioinformatics containers
genomeview
An extensible python-based genomics visualization engine
Mendieta.C4_manuscript
Code used for the analysis of C4 cis-regulatory elements.
Mendieta_Dissertation_github
Supplamental Figures and Tables for Pablo Mendieta's Dissertation 2024
Multilevel_Modeling
Data and code used in paper: Students are rarely independent: When, why, and how to use random effects in discipline-based education research
nf-repeatmasking
Nextflow workflow for automatic repeat detection, classification and masking
NoMoreScripting
I am sick of writing the same parsers day after day. So this module seeks to minimize my time writing the same files again and again
sctransform
R package for modeling single cell UMI expression data using regularized negative binomial regression
shiny_popgen
Shiny apps for teaching Population Genetics
SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
Tiberius-
A simple script to go through the output of an Apollo Annotation and return only filed with a "good" start codon "M".
vim-snippets
vim-snipmate default snippets (Previously snipmate-snippets)