Pinned Repositories
AGP_scripts
Algorithms-Design-and-Analysis-Part-1
all programming assignments and quiz of course offered by Stanford University in Coursera
AlgorithmsForMolecularBiology
All homeworks and created scripts for CU's Algorithms for Molecular biology course
Annotation-Tools
Scripts and tools to assist annotation.
Apple_GATK_Scripts
Augustus_Training
Scripts to train augustus software using PASA pipeline output files.
Basics-VIMRC-TMUX
IntronExonFetcher
A python script to get intron and exon files from a fasta file with multiple genomic scaffolds as well as
MendietaPablo_Annotation_Paper_scripts
Scripts used for analysis and pipline of Mendieta et al 2020
Jome0169's Repositories
Jome0169/Augustus_Training
Scripts to train augustus software using PASA pipeline output files.
Jome0169/MendietaPablo_Annotation_Paper_scripts
Scripts used for analysis and pipline of Mendieta et al 2020
Jome0169/AGP_scripts
Jome0169/Annotation-Tools
Scripts and tools to assist annotation.
Jome0169/Apple_GATK_Scripts
Jome0169/BioinformaticsScripts
An improved Repo of usful scrips for various scripts I have designed to work with NGS data. Scripts are free to use
Jome0169/biopython
Official git repository for Biopython (converted from CVS)
Jome0169/cv
My Curriculum vitae
Jome0169/dotfiles
Jome0169/dragonn
A toolkit to learn how to model and interpret regulatory sequence data using deep learning.
Jome0169/FinalTerpPush
Jome0169/genomeview
An extensible python-based genomics visualization engine
Jome0169/GRFP
Here are a set of example Relevant Background and Future Goals and Graduate Research Plan Statement statements for the NSF GRFP in Ecology and Evolutionary Biology.
Jome0169/iTAK
iTAK
Jome0169/iterm2-Tmux-Vimrc
Jome0169/Jome0169.github.io
Jome0169/Mendieta.C4_manuscript
Code used for the analysis of C4 cis-regulatory elements.
Jome0169/Mendieta.DeepLearning.CREs
Repo for the analysis of cell-type-specific CREs in plants generally. Seeing what we can learn
Jome0169/Mendieta_Dissertation_github
Supplamental Figures and Tables for Pablo Mendieta's Dissertation 2024
Jome0169/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
Jome0169/nf-repeatmasking
Nextflow workflow for automatic repeat detection, classification and masking
Jome0169/NGSWorkflows-
Jome0169/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
Jome0169/sctransform
R package for modeling single cell UMI expression data using regularized negative binomial regression
Jome0169/shiny_popgen
Shiny apps for teaching Population Genetics
Jome0169/SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
Jome0169/Socrates
Jome0169/SyntenicBlockFinder
Jome0169/Tiberius-
A simple script to go through the output of an Apollo Annotation and return only filed with a "good" start codon "M".
Jome0169/vim-snippets
vim-snipmate default snippets (Previously snipmate-snippets)