Discover WGLab/LongReadSum 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

C++

LongGF

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

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

NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data

NanoRepeat

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

C++

mutformer

A transformer model to predict pathogenic mutations

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

C++

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