Sh1ne111

MAC

Merging assemblies by using adjacency algebraic model and classification

hapdiff

SV calling for diploid assemblies

mpQTL

github repository for R package mpQTL

BioSeqUtils

Extract Sequence from Genome According to Annotation File

HMMploidy

A tool to calculate ploidy levels from genotype likelihoods and coverage using Hidden Markov Models

Trinotate

Trinotate source code

khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

TOGA

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

pedigreeSim

PedigreeSim is software that generates simulated genetic marker data of individuals in pedigreed populations. A population can consist of either diploid or tetraploid individuals. PedigreeSim can simulate meioses with or without chiasma interference, and in tetraploids it can simulate meioses with two bivalents or one quadrivalent per set of hom(oe)ologous chromosomes. Also varying probabilities of preferential versus random pairing of chromosomes can be simulated, allowing to simulate amphidiploids as well as autotetraploids and intermediate forms.

TALE

Transformer-based protein function Annotation with joint feature-Label Embedding

docker-4dn-hic

Docker for 4DN Hi-C processing pipeline

vcf_line_splitter

Split a huge VCF file into parts, quickly

LongRepMarker

LongRepMarker: A high-precision algorithm for marking long repeat regions in genomes

GenometracksByGenotype

Helper script to plot molQTLs. Normalize and group bigwigs by genotype.

tackPlotR

An R package to visualize bigwigs.

clocus

A R package to plot a more fancy locuszoom plot/

remap-gff3

update gff3 coordinates to new assembly versions

homotools

Deep_learning_examples

Examples of using deep learning in Bioinformatics

bio_scripts

sharing scripts

CNSTools

Tools for conserved non-coding sequence identification

Camoco

Camoco is a fully-fledged software package for building co-expression networks and analyzing the overlap interactions among genes.

vg_snakemake

Snakemake workflow for the vg toolkit.

AlphaMME

R package for fitting simple genomic selection models

vgrna-project-paper

Bash scripts and data used in pantranscriptomic paper

PECAT

PECAT, a phased error correct and assembly tool

elprep

elPrep: a high-performance tool for analyzing sequence alignment/map files in sequencing pipelines.

CAPG

HAPLOSWEEP

Haplotype-based genotyping designed for polyploid species

DLpipeline

Practical Deep Learning for Genomic Prediction: A Keras based guide to implement deep learning