TrevorKrabbenhoft's Stars
marcpaga/esox
Ensiuc/DMRichr
A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)
kiranbandi/synvisio
SynVisio is an interactive multiscale visualization tool that lets you explore the results of McScanX a popular synteny and collinearity detection toolkit.
ProteomicsML/ProteomicsML
Community-curated tutorials and datasets for ML in proteomics
lbcb-sci/herro
HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).
ngphubinh/enhancers
iEnhancer-ECNN: Identifying Enhancers and their Strength using Ensembles of Convolutional Neural Networks
henryjuho/sal_enhancers
DFE analysis pipeline from Verta et al. (2021).
tolkit/telomeric-identifier
Identify and find telomeres, or telomeric repeats in a genome.
nclark-lab/RERconverge
Analysis of convergence between organismal traits and DNA/protein sequences
nanoporetech/modkit
A bioinformatics tool for working with modified bases
mrvollger/StainedGlass
Make colorful identity heatmaps of genomic sequence
mrvollger/SafFire
sudmantlab/loco-pipe
loco-pipe is an automated Snakemake pipeline that streamlines a set of essential population genomic analyses for low-coverage whole genome sequencing (lcWGS) data
KrabbenhoftLab/genome_annotation_pipeline
Krabbenhoft Lab genome annotation pipeline using BRAKER and GeMoMa
PeterMulhair/HbxFinder
Pipeline for homeobox gene identification
hiruna72/squigualiser
Visualise and analyse nanopore (ONT) raw signals
al2na/methylKit
R package for DNA methylation analysis
paoloshasta/shasta
De novo assembly from Oxford Nanopore reads.
zhangrengang/SubPhaser
Phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.
refresh-bio/agc
Assembled Genomes Compressor
DessimozLab/matreex
BGI-Qingdao/TGS-GapCloser
A gap-closing software tool that uses long reads to enhance genome assembly.
nanoporetech/duplex-tools
Splitting of sequence reads by internal adapter sequence search
isaacovercast/easySFS
Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis
cmdcolin/awesome-genome-visualization
A list of interesting genome browser or genome-browser-like implementations
nanoporetech/dorado
Oxford Nanopore's Basecaller
epi2me-labs/wf-human-variation
popgenmethods/LDhelmet
Software package for estimating fine-scale recombination rate.
jcerca/Papers
mahulchak/quickmerge
A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.