cgroza

BarcodeAsm

bifrost_jaccard

Compute jaccard similarity matrix between colors in a bifrost compacted colored de Bruijn graph.

dotfiles

Emacs-apt

Apt packager interface for emacs.

gEcrit

gEcrit is a Python IDE. Its focus is on simplicity and ease of use. It is fast and lightweight. It features Python indentation, line numbers, code folding, syntax highlighting, shell access, code completion, a program runner, a source browser, indentation guides, a white space indicator, autosaving, an edge line, multiple tabs, printing, jumping to a specific line, word searching, word replacement, zooming undo/redo, pastebin.com code submission, Python syntax checking, the ability to change the indentation of many lines at once, autocompletiton,file tree browser,and bad brace checking.

GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

KU_tutorial_2023

panmethyl

Map Pacbio methylation data to genome graphs.

SeqLib

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

wx-Youtube

A youtube video downloader.

cgroza/GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

cgroza/KU_tutorial_2023

cgroza/panmethyl

Map Pacbio methylation data to genome graphs.

cgroza/personalized_genomes_gbio

cgroza/pggb

the pangenome graph builder

cgroza/repeatR

read and analyse RepeatMasker output

cgroza/BarcodeAsm

cgroza/bifrost_jaccard

Compute jaccard similarity matrix between colors in a bifrost compacted colored de Bruijn graph.

cgroza/Biomorph

Biomorph program written in Java that aims to simulate evolution by mutation and natural selection with polygons and a turn function.

cgroza/dotfiles

cgroza/nextflow_scripts

cgroza/SeqLib

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

cgroza/arxiv-latex-cleaner

arXiv LaTeX Cleaner: Easily clean the LaTeX code of your paper to submit to arXiv

cgroza/Bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

cgroza/cgroza.github.io

cgroza/cljgfa

Clojure parser for GFA2 format.

cgroza/ConvolutionDrugClassifier

Convolutional neural network drug classifer.

cgroza/CrossMap

CrossMap is a python program to lift over genome coordinates from one genome version to another.

cgroza/gcloud_nextflow

Nextflow pipeline for SURVIVOR.

cgroza/graph_peak_caller

ChIP-seq peak caller for reads mapped to a graph-based reference genome

cgroza/hifiasm_nextflow

cgroza/minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

cgroza/NanoVar

Structural variant caller for low-depth long-read sequencing data

cgroza/nearestpaths

Find nearest paths in a genome graph

cgroza/pangenie_nextflow

Nextflow script to run PanGenie on thousands of samples.

cgroza/sane-mmtag

Program that parses base modifications data in BAM files and outputs read annotations in sane BED-like coordinates.

cgroza/smoothxg

linearize and simplify variation graphs using blocked partial order alignment

cgroza/sv_segway

cgroza/svaba

Structural variation and indel detection by local assembly

cgroza/twauctex

Tweaks for AUCtex