shangshanzhizhe

tf_unet

Generic U-Net Tensorflow implementation for image segmentation

github-activity-readme

Updates README with the recent GitHub activity of a user

seqio

Task-based datasets, preprocessing, and evaluation for sequence models.

abyss

:microscope: Assemble large genomes using short reads

pybedtools

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

scikit-fmm

scikit-fmm is a Python extension module which implements the fast marching method.

purge_dups

haplotypic duplication identification tool

IsoSeq

Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

rmats2sashimiplot

odp

oxford dot plots

pbsv

pbsv - PacBio structural variant (SV) calling and analysis tools

learning_bam_file

Learning the Sequence Alignment/Map format

infernal

RNA secondary structure/sequence profiles for homology search and alignment

pangenie

Pangenome-based genome inference

arcs

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

pav

Phased assembly variant caller

pangraph

A bioinformatic toolkit to align genome assemblies into pangenome graphs

DeepTE

Neural network classification of TE

panacus

Panacus is a tool for computing statistics for GFA-formatted pangenome graphs

FLAMES

Full-length transcriptome splicing and mutation analysis

shapeit5

Segmented HAPlotype Estimation and Imputation Tool

HiPhase

Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads

tRNAscan-SE

A program for detection of tRNA genes

panGraphViewer

Show pangenome graphs in an easy way

LongStitch

Correct and scaffold assemblies using long reads

GFAffix

GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.

gimbricate

recompute GFA link overlaps

Fast-Marching-Image-Segmentation

Image segmentation method based on the fast marching method

size-and-shape-of-insect-wings

Code accompanying "Size and shape of insect wings" by M. Salcedo, J. Hoffmann, S. Donoughe, and L. Mahadevan.

SBM-tools