shangshanzhizhe

hmmlearn

Hidden Markov Models in Python, with scikit-learn like API

tf_unet

Generic U-Net Tensorflow implementation for image segmentation

csvtk

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

VesselSeg-Pytorch

Retinal vessel segmentation toolkit based on pytorch

gw

Genome browser and variant annotation

scikit-fmm

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

Winnowmap

Long read / genome alignment software

dotPlotly

Generate an interactive dot plot from mummer or minimap alignments

chromap

Fast alignment and preprocessing of chromatin profiles

IsoSeq

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

wfmash

base-accurate DNA sequence alignments using WFA and mashmap3

GALBA

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several closely related species are available.

tama

Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)

learning_bam_file

Learning the Sequence Alignment/Map format

pgr-tk

PGR-TK: Pangenome Research Tool Kit

ggCaller

Bifrost graph gene caller.

SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances

rustybam

bioinformatics toolkit in rust

dna-nn

Model and predict short DNA sequence features with neural networks

HiPhase

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

tRNAscan-SE

A program for detection of tRNA genes

DeBreak

Structural variant caller for real-time long-read sequencing data

T1K

T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with bulk or single-cell RNA-seq, WGS or WES data.

LIONS

LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts

asynt

Genome alignment and synteny plots

Fast-Marching-Image-Segmentation

Image segmentation method based on the fast marching method

PhyloNet

SVJedi-graph

SV genotyper for long reads with a variation graph

wrath

Wrath: WRapped Analysis of Tagged Haplotypes

size-and-shape-of-insect-wings

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