Discover WGLab/NanoRepeat Open Source project

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications

188

dragonstar2019

135

DeepMod

Variant calling tool for long-read sequencing data

NanoCaller

Copy number vaiation detection from SNP arrays

PennCNV

biocluster

Tutorial on building a computing cluster for bioinformatics

phenolyzer

phenotype-based prioritization of candidate genes for human diseases

Bioformer: an efficient BERT model for biomedical text mining

Bioformer

VirTect

Detection of viruses from RNA-Seq on human samples

Phenotype driven gene prioritization for HPO

Phen2Gene

Clinical interpretation of somatic mutations in cancer

CancerVar

Long-read Isoform Quantification and Analysis

LIQA

NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data

NanoMod

A pipeline that takes clinical notes from EHRs and generate phenotype terms, then generate ranked gene list

EHR-Phenolyzer

a hidden Markov model to infer simple repeats from genome sequences

RepeatHMM

DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads

DeepMod2

Automated human exome/genome variants detection from FASTQ files

SeqMule

A computational algorithm and software tool for fast and accurate detection of gene fusion by long-read transcriptome sequencing

LongGF

Workshop_Annotation

Course materials for "Variants Annotate and Phenotype Analysis"

LinkedSV

GenGen

A set of software tools to facilitate GWAS analysis

DeepRepeat

An accurate repeat detection from Nanopore data using deep learning and image techniques

HadoopCNV

HadoopCNV is a MapReduce-based copy number variation caller for genome sequencing data

Java

lncScore

A python package for the identification of lncRNA from the assembled novel transcripts

PhenoSV: Interpretable phenotype-aware model for the prioritization of genes affected by structural variants.

PhenoSV

PhenoGPT

Group lasso based Deep Neural Network for Cancer Prognosis

GDP

iCAGES (integrated CAncer GEnome Score) is an effective tool for prioritizing cancer driver genes for a patient

icages

A software package for detection of copy number alterations from tumor samples

PennCNV2

LongReadSum

A transformer model to predict pathogenic mutations

mutformer

Simulator for structural variants in various types of next-generation sequencing data

SVGen

A barcode demultiplexer for Oxford Nanopore long-read amplicon sequencing data

AmpBinner

DELongSeq

integrated Mental-disorder Genome Score

iMEGES

UROBORUS: circular RNA identification from RNA-Seq data

UROBORUS

epilepsy-autism-multiplex-network

Development of phencards.org web server for one stop shop of phenotype information

PhenCards

HTML

PennCNV-Seq

Adaption of the original PennCNV algorithm for whole-genome sequencing data

uniline

Assembly-based analysis

kgev-neo4j

web server of 4C-Seq data analysis pipeline

QuantitativeGenomics2022

w4CSeq

NanoBinner

Phen2Gene improved and optimized for pipelines

Phen2Gene2

An alignment-based, generalized structural variant caller for long-read sequencing/mapping data

ContextSV

ASD_terminology

Project_Belka

Materials for Quantitative Genomics 2023 workshop

QuantitativeGenomics2023

SGAN

SGAN (Oncogenicity score prediction using Semi-supervised Generative Adversarial Networks)

Prediction of lncRNA from RNA-Seq data

QuantitativeGenomics2021

lncScore-Java

Java

HTT-SNP-Phasing

icages-server

the iCAGES server running on Ruby on Rails

JavaScript

GestaltMML

Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencing

SCOTCH