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doc-ANNOVAR
Documentation for the ANNOVAR softwareInterVar
A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guidelinedragonstar2019
DeepMod
DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modificationsNanoCaller
Variant calling tool for long-read sequencing dataPennCNV
Copy number vaiation detection from SNP arraysbiocluster
Tutorial on building a computing cluster for bioinformaticsphenolyzer
phenotype-based prioritization of candidate genes for human diseasesBioformer
Bioformer: an efficient BERT model for biomedical text miningVirTect
Detection of viruses from RNA-Seq on human samplesPhen2Gene
Phenotype driven gene prioritization for HPOCancerVar
Clinical interpretation of somatic mutations in cancerLIQA
Long-read Isoform Quantification and AnalysisNanoMod
NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing dataEHR-Phenolyzer
A pipeline that takes clinical notes from EHRs and generate phenotype terms, then generate ranked gene listRepeatHMM
a hidden Markov model to infer simple repeats from genome sequencesDeepMod2
DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore readsSeqMule
Automated human exome/genome variants detection from FASTQ filesLongGF
A computational algorithm and software tool for fast and accurate detection of gene fusion by long-read transcriptome sequencingWorkshop_Annotation
Course materials for "Variants Annotate and Phenotype Analysis"LinkedSV
GenGen
A set of software tools to facilitate GWAS analysisDeepRepeat
An accurate repeat detection from Nanopore data using deep learning and image techniquesHadoopCNV
HadoopCNV is a MapReduce-based copy number variation caller for genome sequencing datalncScore
A python package for the identification of lncRNA from the assembled novel transcriptsPhenoSV
PhenoSV: Interpretable phenotype-aware model for the prioritization of genes affected by structural variants.PhenoGPT
GDP
Group lasso based Deep Neural Network for Cancer PrognosisNanoRepeat
NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing dataicages
iCAGES (integrated CAncer GEnome Score) is an effective tool for prioritizing cancer driver genes for a patientPennCNV2
A software package for detection of copy number alterations from tumor samplesLongReadSum
mutformer
A transformer model to predict pathogenic mutationsSVGen
Simulator for structural variants in various types of next-generation sequencing dataDELongSeq
iMEGES
integrated Mental-disorder Genome ScoreUROBORUS
UROBORUS: circular RNA identification from RNA-Seq dataepilepsy-autism-multiplex-network
PhenCards
Development of phencards.org web server for one stop shop of phenotype informationPennCNV-Seq
Adaption of the original PennCNV algorithm for whole-genome sequencing datauniline
Assembly-based analysiskgev-neo4j
QuantitativeGenomics2022
w4CSeq
web server of 4C-Seq data analysis pipelineNanoBinner
Phen2Gene2
Phen2Gene improved and optimized for pipelinesContextSV
An alignment-based, generalized structural variant caller for long-read sequencing/mapping dataASD_terminology
Project_Belka
QuantitativeGenomics2023
Materials for Quantitative Genomics 2023 workshopSGAN
SGAN (Oncogenicity score prediction using Semi-supervised Generative Adversarial Networks)QuantitativeGenomics2021
lncScore-Java
Prediction of lncRNA from RNA-Seq dataHTT-SNP-Phasing
icages-server
the iCAGES server running on Ruby on RailsGestaltMML
SCOTCH
Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencingLove Open Source and this site? Check out how you can help us